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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/share/man/man1/samtools.1 @ 68:5028fdace37b
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| author | jpayne |
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| date | Tue, 18 Mar 2025 16:23:26 -0400 |
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| 1 '\" t | |
| 2 .TH samtools 1 "21 June 2017" "samtools-1.5" "Bioinformatics tools" | |
| 3 .SH NAME | |
| 4 samtools \- Utilities for the Sequence Alignment/Map (SAM) format | |
| 5 .\" | |
| 6 .\" Copyright (C) 2008-2011, 2013-2017 Genome Research Ltd. | |
| 7 .\" Portions copyright (C) 2010, 2011 Broad Institute. | |
| 8 .\" | |
| 9 .\" Author: Heng Li <lh3@sanger.ac.uk> | |
| 10 .\" Author: Joshua C. Randall <jcrandall@alum.mit.edu> | |
| 11 .\" | |
| 12 .\" Permission is hereby granted, free of charge, to any person obtaining a | |
| 13 .\" copy of this software and associated documentation files (the "Software"), | |
| 14 .\" to deal in the Software without restriction, including without limitation | |
| 15 .\" the rights to use, copy, modify, merge, publish, distribute, sublicense, | |
| 16 .\" and/or sell copies of the Software, and to permit persons to whom the | |
| 17 .\" Software is furnished to do so, subject to the following conditions: | |
| 18 .\" | |
| 19 .\" The above copyright notice and this permission notice shall be included in | |
| 20 .\" all copies or substantial portions of the Software. | |
| 21 .\" | |
| 22 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 23 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 24 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL | |
| 25 .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 26 .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING | |
| 27 .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER | |
| 28 .\" DEALINGS IN THE SOFTWARE. | |
| 29 . | |
| 30 .\" For code blocks and examples (cf groff's Ultrix-specific man macros) | |
| 31 .de EX | |
| 32 | |
| 33 . in +\\$1 | |
| 34 . nf | |
| 35 . ft CR | |
| 36 .. | |
| 37 .de EE | |
| 38 . ft | |
| 39 . fi | |
| 40 . in | |
| 41 | |
| 42 .. | |
| 43 . | |
| 44 .SH SYNOPSIS | |
| 45 .PP | |
| 46 samtools view -bt ref_list.txt -o aln.bam aln.sam.gz | |
| 47 .PP | |
| 48 samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam | |
| 49 .PP | |
| 50 samtools index aln.sorted.bam | |
| 51 .PP | |
| 52 samtools idxstats aln.sorted.bam | |
| 53 .PP | |
| 54 samtools flagstat aln.sorted.bam | |
| 55 .PP | |
| 56 samtools stats aln.sorted.bam | |
| 57 .PP | |
| 58 samtools bedcov aln.sorted.bam | |
| 59 .PP | |
| 60 samtools depth aln.sorted.bam | |
| 61 .PP | |
| 62 samtools view aln.sorted.bam chr2:20,100,000-20,200,000 | |
| 63 .PP | |
| 64 samtools merge out.bam in1.bam in2.bam in3.bam | |
| 65 .PP | |
| 66 samtools faidx ref.fasta | |
| 67 .PP | |
| 68 samtools tview aln.sorted.bam ref.fasta | |
| 69 .PP | |
| 70 samtools split merged.bam | |
| 71 .PP | |
| 72 samtools quickcheck in1.bam in2.cram | |
| 73 .PP | |
| 74 samtools dict -a GRCh38 -s "Homo sapiens" ref.fasta | |
| 75 .PP | |
| 76 samtools fixmate in.namesorted.sam out.bam | |
| 77 .PP | |
| 78 samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam | |
| 79 .PP | |
| 80 samtools flags PAIRED,UNMAP,MUNMAP | |
| 81 .PP | |
| 82 samtools fastq input.bam > output.fastq | |
| 83 .PP | |
| 84 samtools fasta input.bam > output.fasta | |
| 85 .PP | |
| 86 samtools addreplacerg -r 'ID:fish' -r 'LB:1334' -r 'SM:alpha' -o output.bam input.bam | |
| 87 .PP | |
| 88 samtools collate aln.sorted.bam aln.name_collated.bam | |
| 89 .PP | |
| 90 samtools depad input.bam | |
| 91 | |
| 92 .SH DESCRIPTION | |
| 93 .PP | |
| 94 Samtools is a set of utilities that manipulate alignments in the BAM | |
| 95 format. It imports from and exports to the SAM (Sequence Alignment/Map) | |
| 96 format, does sorting, merging and indexing, and allows to retrieve reads | |
| 97 in any regions swiftly. | |
| 98 | |
| 99 Samtools is designed to work on a stream. It regards an input file `-' | |
| 100 as the standard input (stdin) and an output file `-' as the standard | |
| 101 output (stdout). Several commands can thus be combined with Unix | |
| 102 pipes. Samtools always output warning and error messages to the standard | |
| 103 error output (stderr). | |
| 104 | |
| 105 Samtools is also able to open a BAM (not SAM) file on a remote FTP or | |
| 106 HTTP server if the BAM file name starts with `ftp://' or `http://'. | |
| 107 Samtools checks the current working directory for the index file and | |
| 108 will download the index upon absence. Samtools does not retrieve the | |
| 109 entire alignment file unless it is asked to do so. | |
| 110 | |
| 111 .SH COMMANDS AND OPTIONS | |
| 112 | |
| 113 .TP 10 \"-------- view | |
| 114 .B view | |
| 115 samtools view | |
| 116 .RI [ options ] | |
| 117 .IR in.sam | in.bam | in.cram | |
| 118 .RI [ region ...] | |
| 119 | |
| 120 With no options or regions specified, prints all alignments in the specified | |
| 121 input alignment file (in SAM, BAM, or CRAM format) to standard output | |
| 122 in SAM format (with no header). | |
| 123 | |
| 124 You may specify one or more space-separated region specifications after the | |
| 125 input filename to restrict output to only those alignments which overlap the | |
| 126 specified region(s). Use of region specifications requires a coordinate-sorted | |
| 127 and indexed input file (in BAM or CRAM format). | |
| 128 | |
| 129 The | |
| 130 .BR -b , | |
| 131 .BR -C , | |
| 132 .BR -1 , | |
| 133 .BR -u , | |
| 134 .BR -h , | |
| 135 .BR -H , | |
| 136 and | |
| 137 .B -c | |
| 138 options change the output format from the default of headerless SAM, and the | |
| 139 .B -o | |
| 140 and | |
| 141 .B -U | |
| 142 options set the output file name(s). | |
| 143 | |
| 144 The | |
| 145 .B -t | |
| 146 and | |
| 147 .B -T | |
| 148 options provide additional reference data. One of these two options is required | |
| 149 when SAM input does not contain @SQ headers, and the | |
| 150 .B -T | |
| 151 option is required whenever writing CRAM output. | |
| 152 | |
| 153 The | |
| 154 .BR -L , | |
| 155 .BR -r , | |
| 156 .BR -R , | |
| 157 .BR -s , | |
| 158 .BR -q , | |
| 159 .BR -l , | |
| 160 .BR -m , | |
| 161 .BR -f , | |
| 162 .BR -F , | |
| 163 and | |
| 164 .B -G | |
| 165 options filter the alignments that will be included in the output to only those | |
| 166 alignments that match certain criteria. | |
| 167 | |
| 168 The | |
| 169 .B -x | |
| 170 and | |
| 171 .B -B | |
| 172 options modify the data which is contained in each alignment. | |
| 173 | |
| 174 Finally, the | |
| 175 .B -@ | |
| 176 option can be used to allocate additional threads to be used for compression, and the | |
| 177 .B -? | |
| 178 option requests a long help message. | |
| 179 | |
| 180 .TP | |
| 181 .B REGIONS: | |
| 182 .RS | |
| 183 Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position | |
| 184 coordinates are 1-based. | |
| 185 | |
| 186 Important note: when multiple regions are given, some alignments may be output | |
| 187 multiple times if they overlap more than one of the specified regions. | |
| 188 | |
| 189 Examples of region specifications: | |
| 190 .TP 10 | |
| 191 .B chr1 | |
| 192 Output all alignments mapped to the reference sequence named `chr1' (i.e. @SQ SN:chr1). | |
| 193 .TP | |
| 194 .B chr2:1000000 | |
| 195 The region on chr2 beginning at base position 1,000,000 and ending at the | |
| 196 end of the chromosome. | |
| 197 .TP | |
| 198 .B chr3:1000-2000 | |
| 199 The 1001bp region on chr3 beginning at base position 1,000 and ending at base | |
| 200 position 2,000 (including both end positions). | |
| 201 .TP | |
| 202 .B '*' | |
| 203 Output the unmapped reads at the end of the file. | |
| 204 (This does not include any unmapped reads placed on a reference sequence | |
| 205 alongside their mapped mates.) | |
| 206 .TP | |
| 207 .B . | |
| 208 Output all alignments. | |
| 209 (Mostly unnecessary as not specifying a region at all has the same effect.) | |
| 210 .RE | |
| 211 | |
| 212 .B OPTIONS: | |
| 213 .RS | |
| 214 .TP 10 | |
| 215 .B -b | |
| 216 Output in the BAM format. | |
| 217 .TP | |
| 218 .B -C | |
| 219 Output in the CRAM format (requires -T). | |
| 220 .TP | |
| 221 .B -1 | |
| 222 Enable fast BAM compression (implies -b). | |
| 223 .TP | |
| 224 .B -u | |
| 225 Output uncompressed BAM. This option saves time spent on | |
| 226 compression/decompression and is thus preferred when the output is piped | |
| 227 to another samtools command. | |
| 228 .TP | |
| 229 .B -h | |
| 230 Include the header in the output. | |
| 231 .TP | |
| 232 .B -H | |
| 233 Output the header only. | |
| 234 .TP | |
| 235 .B -c | |
| 236 Instead of printing the alignments, only count them and print the | |
| 237 total number. All filter options, such as | |
| 238 .BR -f , | |
| 239 .BR -F , | |
| 240 and | |
| 241 .BR -q , | |
| 242 are taken into account. | |
| 243 .TP | |
| 244 .B -? | |
| 245 Output long help and exit immediately. | |
| 246 .TP | |
| 247 .BI "-o " FILE | |
| 248 Output to | |
| 249 .I FILE [stdout]. | |
| 250 .TP | |
| 251 .BI "-U " FILE | |
| 252 Write alignments that are | |
| 253 .I not | |
| 254 selected by the various filter options to | |
| 255 .IR FILE . | |
| 256 When this option is used, all alignments (or all alignments intersecting the | |
| 257 .I regions | |
| 258 specified) are written to either the output file or this file, but never both. | |
| 259 .TP | |
| 260 .BI "-t " FILE | |
| 261 A tab-delimited | |
| 262 .IR FILE . | |
| 263 Each line must contain the reference name in the first column and the length of | |
| 264 the reference in the second column, with one line for each distinct reference. | |
| 265 Any additional fields beyond the second column are ignored. This file also | |
| 266 defines the order of the reference sequences in sorting. If you run: | |
| 267 `samtools faidx <ref.fa>', the resulting index file | |
| 268 .I <ref.fa>.fai | |
| 269 can be used as this | |
| 270 .IR FILE . | |
| 271 .TP | |
| 272 .BI "-T " FILE | |
| 273 A FASTA format reference | |
| 274 .IR FILE , | |
| 275 optionally compressed by | |
| 276 .B bgzip | |
| 277 and ideally indexed by | |
| 278 .B samtools | |
| 279 .BR faidx . | |
| 280 If an index is not present, one will be generated for you. | |
| 281 .TP | |
| 282 .BI "-L " FILE | |
| 283 Only output alignments overlapping the input BED | |
| 284 .I FILE | |
| 285 [null]. | |
| 286 .TP | |
| 287 .BI "-r " STR | |
| 288 Only output alignments in read group | |
| 289 .I STR | |
| 290 [null]. | |
| 291 .TP | |
| 292 .BI "-R " FILE | |
| 293 Output alignments in read groups listed in | |
| 294 .I FILE | |
| 295 [null]. | |
| 296 .TP | |
| 297 .BI "-q " INT | |
| 298 Skip alignments with MAPQ smaller than | |
| 299 .I INT | |
| 300 [0]. | |
| 301 .TP | |
| 302 .BI "-l " STR | |
| 303 Only output alignments in library | |
| 304 .I STR | |
| 305 [null]. | |
| 306 .TP | |
| 307 .BI "-m " INT | |
| 308 Only output alignments with number of CIGAR bases consuming query | |
| 309 sequence \(>= | |
| 310 .I INT | |
| 311 [0] | |
| 312 .TP | |
| 313 .BI "-f " INT | |
| 314 Only output alignments with all bits set in | |
| 315 .I INT | |
| 316 present in the FLAG field. | |
| 317 .I INT | |
| 318 can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) | |
| 319 or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]. | |
| 320 .TP | |
| 321 .BI "-F " INT | |
| 322 Do not output alignments with any bits set in | |
| 323 .I INT | |
| 324 present in the FLAG field. | |
| 325 .I INT | |
| 326 can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) | |
| 327 or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]. | |
| 328 .TP | |
| 329 .BI "-G " INT | |
| 330 Do not output alignments with all bits set in | |
| 331 .I INT | |
| 332 present in the FLAG field. This is the opposite of \fI-f\fR such | |
| 333 that \fI-f12 -G12\fR is the same as no filtering at all. | |
| 334 .I INT | |
| 335 can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) | |
| 336 or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]. | |
| 337 .TP | |
| 338 .BI "-x " STR | |
| 339 Read tag to exclude from output (repeatable) [null] | |
| 340 .TP | |
| 341 .B -B | |
| 342 Collapse the backward CIGAR operation. | |
| 343 .TP | |
| 344 .BI "-s " FLOAT | |
| 345 Output only a proportion of the input alignments. | |
| 346 This subsampling acts in the same way on all of the alignment records in | |
| 347 the same template or read pair, so it never keeps a read but not its mate. | |
| 348 .IP | |
| 349 The integer and fractional parts of the | |
| 350 .BI "-s " INT . FRAC | |
| 351 option are used separately: the part after the | |
| 352 decimal point sets the fraction of templates/pairs to be kept, | |
| 353 while the integer part is used as a seed that influences | |
| 354 .I which | |
| 355 subset of reads is kept. | |
| 356 .IP | |
| 357 .\" Reads are retained based on a score computed by hashing their QNAME | |
| 358 .\" field and the seed value. | |
| 359 When subsampling data that has previously been subsampled, be sure to use | |
| 360 a different seed value from those used previously; otherwise more reads | |
| 361 will be retained than expected. | |
| 362 .TP | |
| 363 .BI "-@ " INT | |
| 364 Number of BAM compression threads to use in addition to main thread [0]. | |
| 365 .TP | |
| 366 .B -S | |
| 367 Ignored for compatibility with previous samtools versions. | |
| 368 Previously this option was required if input was in SAM format, but now the | |
| 369 correct format is automatically detected by examining the first few characters | |
| 370 of input. | |
| 371 .RE | |
| 372 | |
| 373 .TP \"-------- sort | |
| 374 .B sort | |
| 375 .na | |
| 376 samtools sort | |
| 377 .RB [ -l | |
| 378 .IR level ] | |
| 379 .RB [ -m | |
| 380 .IR maxMem ] | |
| 381 .RB [ -o | |
| 382 .IR out.bam ] | |
| 383 .RB [ -O | |
| 384 .IR format ] | |
| 385 .RB [ -n ] | |
| 386 .RB [ -t | |
| 387 .IR tag ] | |
| 388 .RB [ -T | |
| 389 .IR tmpprefix ] | |
| 390 .RB [ -@ | |
| 391 .IR threads "] [" in.sam | in.bam | in.cram ] | |
| 392 .ad | |
| 393 | |
| 394 Sort alignments by leftmost coordinates, or by read name when | |
| 395 .B -n | |
| 396 is used. | |
| 397 An appropriate | |
| 398 .B @HD-SO | |
| 399 sort order header tag will be added or an existing one updated if necessary. | |
| 400 | |
| 401 The sorted output is written to standard output by default, or to the | |
| 402 specified file | |
| 403 .RI ( out.bam ) | |
| 404 when | |
| 405 .B -o | |
| 406 is used. | |
| 407 This command will also create temporary files | |
| 408 .IB tmpprefix . %d .bam | |
| 409 as needed when the entire alignment data cannot fit into memory | |
| 410 (as controlled via the | |
| 411 .B -m | |
| 412 option). | |
| 413 | |
| 414 .B Options: | |
| 415 .RS | |
| 416 .TP 11 | |
| 417 .BI "-l " INT | |
| 418 Set the desired compression level for the final output file, ranging from 0 | |
| 419 (uncompressed) or 1 (fastest but minimal compression) to 9 (best compression | |
| 420 but slowest to write), similarly to | |
| 421 .BR gzip (1)'s | |
| 422 compression level setting. | |
| 423 .IP | |
| 424 If | |
| 425 .B -l | |
| 426 is not used, the default compression level will apply. | |
| 427 .TP | |
| 428 .BI "-m " INT | |
| 429 Approximately the maximum required memory per thread, specified either in bytes | |
| 430 or with a | |
| 431 .BR K ", " M ", or " G | |
| 432 suffix. | |
| 433 [768 MiB] | |
| 434 .IP | |
| 435 To prevent sort from creating a huge number of temporary files, it enforces a | |
| 436 minimum value of 1M for this setting. | |
| 437 .TP | |
| 438 .B -n | |
| 439 Sort by read names (i.e., the | |
| 440 .B QNAME | |
| 441 field) rather than by chromosomal coordinates. | |
| 442 .TP | |
| 443 .BI "-t " TAG | |
| 444 Sort first by the value in the alignment tag TAG, then by position or name (if | |
| 445 also using \fB-n\fP). | |
| 446 .BI "-o " FILE | |
| 447 Write the final sorted output to | |
| 448 .IR FILE , | |
| 449 rather than to standard output. | |
| 450 .TP | |
| 451 .BI "-O " FORMAT | |
| 452 Write the final output as | |
| 453 .BR sam ", " bam ", or " cram . | |
| 454 | |
| 455 By default, samtools tries to select a format based on the | |
| 456 .B -o | |
| 457 filename extension; if output is to standard output or no format can be | |
| 458 deduced, | |
| 459 .B bam | |
| 460 is selected. | |
| 461 .TP | |
| 462 .BI "-T " PREFIX | |
| 463 Write temporary files to | |
| 464 .IB PREFIX . nnnn .bam, | |
| 465 or if the specified | |
| 466 .I PREFIX | |
| 467 is an existing directory, to | |
| 468 .IB PREFIX /samtools. mmm . mmm .tmp. nnnn .bam, | |
| 469 where | |
| 470 .I mmm | |
| 471 is unique to this invocation of the | |
| 472 .B sort | |
| 473 command. | |
| 474 .IP | |
| 475 By default, any temporary files are written alongside the output file, as | |
| 476 .IB out.bam .tmp. nnnn .bam, | |
| 477 or if output is to standard output, in the current directory as | |
| 478 .BI samtools. mmm . mmm .tmp. nnnn .bam. | |
| 479 .TP | |
| 480 .BI "-@ " INT | |
| 481 Set number of sorting and compression threads. | |
| 482 By default, operation is single-threaded. | |
| 483 .PP | |
| 484 .B Ordering Rules | |
| 485 | |
| 486 The following rules are used for ordering records. | |
| 487 | |
| 488 If option \fB-t\fP is in use, records are first sorted by the value of | |
| 489 the given alignment tag, and then by position or name (if using \fB-n\fP). | |
| 490 For example, \*(lq-t RG\*(rq will make read group the primary sort key. The | |
| 491 rules for ordering by tag are: | |
| 492 | |
| 493 .IP \(bu 4 | |
| 494 Records that do not have the tag are sorted before ones that do. | |
| 495 .IP \(bu 4 | |
| 496 If the types of the tags are different, they will be sorted so | |
| 497 that single character tags (type A) come before array tags (type B), then | |
| 498 string tags (types H and Z), then numeric tags (types f and i). | |
| 499 .IP \(bu 4 | |
| 500 Numeric tags (types f and i) are compared by value. Note that comparisons | |
| 501 of floating-point values are subject to issues of rounding and precision. | |
| 502 .IP \(bu 4 | |
| 503 String tags (types H and Z) are compared based on the binary | |
| 504 contents of the tag using the C | |
| 505 .BR strcmp (3) | |
| 506 function. | |
| 507 .IP \(bu 4 | |
| 508 Character tags (type A) are compared by binary character value. | |
| 509 .IP \(bu 4 | |
| 510 No attempt is made to compare tags of other types \(em notably type B | |
| 511 array values will not be compared. | |
| 512 .PP | |
| 513 When the \fB-n\fP option is present, records are sorted by name. Names are | |
| 514 compared so as to give a \*(lqnatural\*(rq ordering \(em i.e. sections | |
| 515 consisting of digits are compared numerically while all other sections are | |
| 516 compared based on their binary representation. This means \*(lqa1\*(rq will | |
| 517 come before \*(lqb1\*(rq and \*(lqa9\*(rq will come before \*(lqa10\*(rq. | |
| 518 Records with the same name will be ordered according to the values of | |
| 519 the READ1 and READ2 flags (see | |
| 520 .BR flags ). | |
| 521 | |
| 522 When the \fB-n\fP option is | |
| 523 .B not | |
| 524 present, reads are sorted by reference (according to the order of the @SQ | |
| 525 header records), then by position in the reference, and then by the REVERSE | |
| 526 flag. | |
| 527 | |
| 528 .B Note | |
| 529 | |
| 530 .PP | |
| 531 Historically | |
| 532 .B samtools sort | |
| 533 also accepted a less flexible way of specifying the final and | |
| 534 temporary output filenames: | |
| 535 .IP | |
| 536 samtools sort | |
| 537 .RB [ -f "] [" -o ] | |
| 538 .I in.bam out.prefix | |
| 539 .PP | |
| 540 This has now been removed. | |
| 541 The previous \fIout.prefix\fP argument (and \fB-f\fP option, if any) | |
| 542 should be changed to an appropriate combination of \fB-T\fP \fIPREFIX\fP | |
| 543 and \fB-o\fP \fIFILE\fP. The previous \fB-o\fP option should be removed, | |
| 544 as output defaults to standard output. | |
| 545 .RE | |
| 546 | |
| 547 .TP \"-------- index | |
| 548 .B index | |
| 549 samtools index | |
| 550 .RB [ -bc ] | |
| 551 .RB [ -m | |
| 552 .IR INT ] | |
| 553 .IR aln.bam | aln.cram | |
| 554 .RI [ out.index ] | |
| 555 | |
| 556 Index a coordinate-sorted BAM or CRAM file for fast random access. | |
| 557 (Note that this does not work with SAM files even if they are bgzip | |
| 558 compressed \(em to index such files, use tabix(1) instead.) | |
| 559 | |
| 560 This index is needed when | |
| 561 .I region | |
| 562 arguments are used to limit | |
| 563 .B samtools view | |
| 564 and similar commands to particular regions of interest. | |
| 565 | |
| 566 If an output filename is given, the index file will be written to | |
| 567 .IR out.index . | |
| 568 Otherwise, for a CRAM file | |
| 569 .IR aln.cram , | |
| 570 index file | |
| 571 .IB aln.cram .crai | |
| 572 will be created; for a BAM file | |
| 573 .IR aln.bam , | |
| 574 either | |
| 575 .IB aln.bam .bai | |
| 576 or | |
| 577 .IB aln.bam .csi | |
| 578 will be created, depending on the index format selected. | |
| 579 | |
| 580 .B Options: | |
| 581 .RS | |
| 582 .TP 8 | |
| 583 .B -b | |
| 584 Create a BAI index. | |
| 585 This is currently the default when no format options are used. | |
| 586 .TP | |
| 587 .B -c | |
| 588 Create a CSI index. | |
| 589 By default, the minimum interval size for the index is 2^14, which is the same | |
| 590 as the fixed value used by the BAI format. | |
| 591 .TP | |
| 592 .BI "-m " INT | |
| 593 Create a CSI index, with a minimum interval size of 2^INT. | |
| 594 .RE | |
| 595 | |
| 596 .TP \"-------- idxstats | |
| 597 .B idxstats | |
| 598 samtools idxstats | |
| 599 .IR in.sam | in.bam | in.cram | |
| 600 | |
| 601 Retrieve and print stats in the index file corresponding to the input file. | |
| 602 Before calling idxstats, the input BAM file must be indexed by samtools index. | |
| 603 | |
| 604 The output is TAB-delimited with each line consisting of reference sequence | |
| 605 name, sequence length, # mapped reads and # unmapped reads. It is written to | |
| 606 stdout. | |
| 607 | |
| 608 .TP \"-------- flagstat | |
| 609 .B flagstat | |
| 610 samtools flagstat | |
| 611 .IR in.sam | in.bam | in.cram | |
| 612 | |
| 613 Does a full pass through the input file to calculate and print statistics | |
| 614 to stdout. | |
| 615 | |
| 616 Provides counts for each of 13 categories based primarily on bit flags in | |
| 617 the FLAG field. Each category in the output is broken down into QC pass and | |
| 618 QC fail, which is presented as "#PASS + #FAIL" followed by a description of | |
| 619 the category. | |
| 620 | |
| 621 The first row of output gives the total number of reads that are QC pass and | |
| 622 fail (according to flag bit 0x200). For example: | |
| 623 | |
| 624 122 + 28 in total (QC-passed reads + QC-failed reads) | |
| 625 | |
| 626 Which would indicate that there are a total of 150 reads in the input file, | |
| 627 122 of which are marked as QC pass and 28 of which are marked as "not passing | |
| 628 quality controls" | |
| 629 | |
| 630 Following this, additional categories are given for reads which are: | |
| 631 | |
| 632 .RS 18 | |
| 633 .TP | |
| 634 secondary | |
| 635 0x100 bit set | |
| 636 .TP | |
| 637 supplementary | |
| 638 0x800 bit set | |
| 639 .TP | |
| 640 duplicates | |
| 641 0x400 bit set | |
| 642 .TP | |
| 643 mapped | |
| 644 0x4 bit not set | |
| 645 .TP | |
| 646 paired in sequencing | |
| 647 0x1 bit set | |
| 648 .TP | |
| 649 read1 | |
| 650 both 0x1 and 0x40 bits set | |
| 651 .TP | |
| 652 read2 | |
| 653 both 0x1 and 0x80 bits set | |
| 654 .TP | |
| 655 properly paired | |
| 656 both 0x1 and 0x2 bits set and 0x4 bit not set | |
| 657 .TP | |
| 658 with itself and mate mapped | |
| 659 0x1 bit set and neither 0x4 nor 0x8 bits set | |
| 660 .TP | |
| 661 singletons | |
| 662 both 0x1 and 0x8 bits set and bit 0x4 not set | |
| 663 .RE | |
| 664 | |
| 665 .RS 10 | |
| 666 And finally, two rows are given that additionally filter on the reference | |
| 667 name (RNAME), mate reference name (MRNM), and mapping quality (MAPQ) fields: | |
| 668 .RE | |
| 669 | |
| 670 .RS 18 | |
| 671 .TP | |
| 672 with mate mapped to a different chr | |
| 673 0x1 bit set and neither 0x4 nor 0x8 bits set and MRNM not equal to RNAME | |
| 674 .TP | |
| 675 with mate mapped to a different chr (mapQ>=5) | |
| 676 0x1 bit set and neither 0x4 nor 0x8 bits set | |
| 677 and MRNM not equal to RNAME and MAPQ >= 5 | |
| 678 .RE | |
| 679 | |
| 680 .TP \"-------- stats | |
| 681 .B stats | |
| 682 samtools stats | |
| 683 .RI [ options ] | |
| 684 .IR in.sam | in.bam | in.cram | |
| 685 .RI [ region ...] | |
| 686 | |
| 687 samtools stats collects statistics from BAM files and outputs in a text format. | |
| 688 The output can be visualized graphically using plot-bamstats. | |
| 689 | |
| 690 .B Options: | |
| 691 .RS | |
| 692 .TP 8 | |
| 693 .BI "-c, --coverage " MIN , MAX , STEP | |
| 694 Set coverage distribution to the specified range (MIN, MAX, STEP all given as integers) | |
| 695 [1,1000,1] | |
| 696 .TP | |
| 697 .B -d, --remove-dups | |
| 698 Exclude from statistics reads marked as duplicates | |
| 699 .TP | |
| 700 .BI "-f, --required-flag " STR "|" INT | |
| 701 Required flag, 0 for unset. See also `samtools flags` | |
| 702 [0] | |
| 703 .TP | |
| 704 .BI "-F, --filtering-flag " STR "|" INT | |
| 705 Filtering flag, 0 for unset. See also `samtools flags` | |
| 706 [0] | |
| 707 .TP | |
| 708 .BI "--GC-depth " FLOAT | |
| 709 the size of GC-depth bins (decreasing bin size increases memory requirement) | |
| 710 [2e4] | |
| 711 .TP | |
| 712 .B -h, --help | |
| 713 This help message | |
| 714 .TP | |
| 715 .BI "-i, --insert-size " INT | |
| 716 Maximum insert size | |
| 717 [8000] | |
| 718 .TP | |
| 719 .BI "-I, --id " STR | |
| 720 Include only listed read group or sample name | |
| 721 [] | |
| 722 .TP | |
| 723 .BI "-l, --read-length " INT | |
| 724 Include in the statistics only reads with the given read length | |
| 725 [] | |
| 726 .TP | |
| 727 .BI "-m, --most-inserts " FLOAT | |
| 728 Report only the main part of inserts | |
| 729 [0.99] | |
| 730 .TP | |
| 731 .BI "-P, --split-prefix " STR | |
| 732 A path or string prefix to prepend to filenames output when creating | |
| 733 categorised statistics files with | |
| 734 .BR -S / --split . | |
| 735 [input filename] | |
| 736 .TP | |
| 737 .BI "-q, --trim-quality " INT | |
| 738 The BWA trimming parameter | |
| 739 [0] | |
| 740 .TP | |
| 741 .BI "-r, --ref-seq " FILE | |
| 742 Reference sequence (required for GC-depth and mismatches-per-cycle calculation). | |
| 743 [] | |
| 744 .TP | |
| 745 .BI "-S, --split " TAG | |
| 746 In addition to the complete statistics, also output categorised statistics | |
| 747 based on the tagged field | |
| 748 .I TAG | |
| 749 (e.g., use | |
| 750 .B --split RG | |
| 751 to split into read groups). | |
| 752 | |
| 753 Categorised statistics are written to files named | |
| 754 .RI < prefix >_< value >.bamstat, | |
| 755 where | |
| 756 .I prefix | |
| 757 is as given by | |
| 758 .B --split-prefix | |
| 759 (or the input filename by default) and | |
| 760 .I value | |
| 761 has been encountered as the specified tagged field's value in one or more | |
| 762 alignment records. | |
| 763 .TP | |
| 764 .BI "-t, --target-regions " FILE | |
| 765 Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive. | |
| 766 [] | |
| 767 .TP | |
| 768 .B "-x, --sparse" | |
| 769 Suppress outputting IS rows where there are no insertions. | |
| 770 .RE | |
| 771 | |
| 772 .TP \"-------- bedcov | |
| 773 .B bedcov | |
| 774 samtools bedcov | |
| 775 .RI [ options ] | |
| 776 .IR region.bed " " in1.sam | in1.bam | in1.cram "[...]" | |
| 777 | |
| 778 Reports the total read base count (i.e. the sum of per base read depths) | |
| 779 for each genomic region specified in the supplied BED file. | |
| 780 Counts for each alignment file supplied are reported in separate columns. | |
| 781 | |
| 782 .B Options: | |
| 783 .RS | |
| 784 .TP | |
| 785 .BI "-Q " INT | |
| 786 .RI "Only count reads with mapping quality greater than " INT | |
| 787 .RE | |
| 788 | |
| 789 .TP \"-------- depth | |
| 790 .B depth | |
| 791 samtools depth | |
| 792 .RI [ options ] | |
| 793 .RI "[" in1.sam | in1.bam | in1.cram " [" in2.sam | in2.bam | in2.cram "] [...]]" | |
| 794 | |
| 795 Computes the depth at each position or region. | |
| 796 | |
| 797 .B Options: | |
| 798 .RS | |
| 799 .TP 8 | |
| 800 .B -a | |
| 801 Output all positions (including those with zero depth) | |
| 802 .TP | |
| 803 .B -a -a, -aa | |
| 804 Output absolutely all positions, including unused reference sequences. | |
| 805 Note that when used in conjunction with a BED file the -a option may | |
| 806 sometimes operate as if -aa was specified if the reference sequence | |
| 807 has coverage outside of the region specified in the BED file. | |
| 808 .TP | |
| 809 .BI "-b " FILE | |
| 810 .RI "Compute depth at list of positions or regions in specified BED " FILE. | |
| 811 [] | |
| 812 .TP | |
| 813 .BI "-f " FILE | |
| 814 .RI "Use the BAM files specified in the " FILE | |
| 815 (a file of filenames, one file per line) | |
| 816 [] | |
| 817 .TP | |
| 818 .BI "-l " INT | |
| 819 .RI "Ignore reads shorter than " INT | |
| 820 .TP | |
| 821 .BI "-m, -d " INT | |
| 822 .RI "Truncate reported depth at a maximum of " INT " reads." | |
| 823 [8000] | |
| 824 .TP | |
| 825 .BI "-q " INT | |
| 826 .RI "Only count reads with base quality greater than " INT | |
| 827 .TP | |
| 828 .BI "-Q " INT | |
| 829 .RI "Only count reads with mapping quality greater than " INT | |
| 830 .TP | |
| 831 .BI "-r " CHR ":" FROM "-" TO | |
| 832 Only report depth in specified region. | |
| 833 .RE | |
| 834 | |
| 835 .TP \"-------- merge | |
| 836 .B merge | |
| 837 samtools merge [-nur1f] [-h inh.sam] [-R reg] [-b <list>] <out.bam> <in1.bam> [<in2.bam> <in3.bam> ... <inN.bam>] | |
| 838 | |
| 839 Merge multiple sorted alignment files, producing a single sorted output file | |
| 840 that contains all the input records and maintains the existing sort order. | |
| 841 | |
| 842 If | |
| 843 .BR -h | |
| 844 is specified the @SQ headers of input files will be merged into the specified header, otherwise they will be merged | |
| 845 into a composite header created from the input headers. If in the process of merging @SQ lines for coordinate sorted | |
| 846 input files, a conflict arises as to the order (for example input1.bam has @SQ for a,b,c and input2.bam has b,a,c) | |
| 847 then the resulting output file will need to be re-sorted back into coordinate order. | |
| 848 | |
| 849 Unless the | |
| 850 .BR -c | |
| 851 or | |
| 852 .BR -p | |
| 853 flags are specified then when merging @RG and @PG records into the output header then any IDs found to be duplicates | |
| 854 of existing IDs in the output header will have a suffix appended to them to differentiate them from similar header | |
| 855 records from other files and the read records will be updated to reflect this. | |
| 856 | |
| 857 The ordering of the records in the input files must match the usage of the | |
| 858 \fB-n\fP and \fB-t\fP command-line options. If they do not, the output | |
| 859 order will be undefined. See | |
| 860 .B sort | |
| 861 for information about record ordering. | |
| 862 | |
| 863 .B OPTIONS: | |
| 864 .RS | |
| 865 .TP 8 | |
| 866 .B -1 | |
| 867 Use zlib compression level 1 to compress the output. | |
| 868 .TP | |
| 869 .BI -b \ FILE | |
| 870 List of input BAM files, one file per line. | |
| 871 .TP | |
| 872 .B -f | |
| 873 Force to overwrite the output file if present. | |
| 874 .TP 8 | |
| 875 .BI -h \ FILE | |
| 876 Use the lines of | |
| 877 .I FILE | |
| 878 as `@' headers to be copied to | |
| 879 .IR out.bam , | |
| 880 replacing any header lines that would otherwise be copied from | |
| 881 .IR in1.bam . | |
| 882 .RI ( FILE | |
| 883 is actually in SAM format, though any alignment records it may contain | |
| 884 are ignored.) | |
| 885 .TP | |
| 886 .B -n | |
| 887 The input alignments are sorted by read names rather than by chromosomal | |
| 888 coordinates | |
| 889 .TP | |
| 890 .B -t TAG | |
| 891 The input alignments have been sorted by the value of TAG, then by either | |
| 892 position or name (if \fB-n\fP is given). | |
| 893 .TP | |
| 894 .BI -R \ STR | |
| 895 Merge files in the specified region indicated by | |
| 896 .I STR | |
| 897 [null] | |
| 898 .TP | |
| 899 .B -r | |
| 900 Attach an RG tag to each alignment. The tag value is inferred from file names. | |
| 901 .TP | |
| 902 .B -u | |
| 903 Uncompressed BAM output | |
| 904 .TP | |
| 905 .B -c | |
| 906 When several input files contain @RG headers with the same ID, emit only one | |
| 907 of them (namely, the header line from the first file we find that ID in) to | |
| 908 the merged output file. | |
| 909 Combining these similar headers is usually the right thing to do when the | |
| 910 files being merged originated from the same file. | |
| 911 | |
| 912 Without \fB-c\fP, all @RG headers appear in the output file, with random | |
| 913 suffixes added to their IDs where necessary to differentiate them. | |
| 914 .TP | |
| 915 .B -p | |
| 916 Similarly, for each @PG ID in the set of files to merge, use the @PG line | |
| 917 of the first file we find that ID in rather than adding a suffix to | |
| 918 differentiate similar IDs. | |
| 919 .RE | |
| 920 | |
| 921 .TP \"-------- faidx | |
| 922 .B faidx | |
| 923 samtools faidx <ref.fasta> [region1 [...]] | |
| 924 | |
| 925 Index reference sequence in the FASTA format or extract subsequence from | |
| 926 indexed reference sequence. If no region is specified, | |
| 927 .B faidx | |
| 928 will index the file and create | |
| 929 .I <ref.fasta>.fai | |
| 930 on the disk. If regions are specified, the subsequences will be | |
| 931 retrieved and printed to stdout in the FASTA format. | |
| 932 | |
| 933 The input file can be compressed in the | |
| 934 .B BGZF | |
| 935 format. | |
| 936 | |
| 937 The sequences in the input file should all have different names. | |
| 938 If they do not, indexing will emit a warning about duplicate sequences and | |
| 939 retrieval will only produce subsequences from the first sequence with the | |
| 940 duplicated name. | |
| 941 | |
| 942 .TP \"-------- tview | |
| 943 .B tview | |
| 944 samtools tview | |
| 945 .RB [ -p | |
| 946 .IR chr:pos ] | |
| 947 .RB [ -s | |
| 948 .IR STR ] | |
| 949 .RB [ -d | |
| 950 .IR display ] | |
| 951 .RI <in.sorted.bam> | |
| 952 .RI [ref.fasta] | |
| 953 | |
| 954 Text alignment viewer (based on the ncurses library). In the viewer, | |
| 955 press `?' for help and press `g' to check the alignment start from a | |
| 956 region in the format like `chr10:10,000,000' or `=10,000,000' when | |
| 957 viewing the same reference sequence. | |
| 958 | |
| 959 .B Options: | |
| 960 .RS | |
| 961 .TP 14 | |
| 962 .BI -d \ display | |
| 963 Output as (H)tml or (C)urses or (T)ext | |
| 964 .TP | |
| 965 .BI -p \ chr:pos | |
| 966 Go directly to this position | |
| 967 .TP | |
| 968 .BI -s \ STR | |
| 969 Display only alignments from this sample or read group | |
| 970 .RE | |
| 971 | |
| 972 .TP \"-------- split | |
| 973 .B split | |
| 974 samtools split | |
| 975 .RI [ options ] | |
| 976 .IR merged.sam | merged.bam | merged.cram | |
| 977 | |
| 978 Splits a file by read group. | |
| 979 | |
| 980 .B Options: | |
| 981 .RS | |
| 982 .TP 14 | |
| 983 .BI "-u " FILE1 | |
| 984 .RI "Put reads with no RG tag or an unrecognised RG tag into " FILE1 | |
| 985 .TP | |
| 986 .BI "-u " FILE1 ":" FILE2 | |
| 987 .RI "As above, but assigns an RG tag as given in the header of " FILE2 | |
| 988 .TP | |
| 989 .BI "-f " STRING | |
| 990 Output filename format string (see below) | |
| 991 ["%*_%#.%."] | |
| 992 .TP | |
| 993 .B -v | |
| 994 Verbose output | |
| 995 .PP | |
| 996 Format string expansions: | |
| 997 .TS | |
| 998 center; | |
| 999 lb l . | |
| 1000 %% % | |
| 1001 %* basename | |
| 1002 %# @RG index | |
| 1003 %! @RG ID | |
| 1004 %. output format filename extension | |
| 1005 .TE | |
| 1006 .RE | |
| 1007 | |
| 1008 .TP \"-------- quickcheck | |
| 1009 .B quickcheck | |
| 1010 samtools quickcheck | |
| 1011 .RI [ options ] | |
| 1012 .IR in.sam | in.bam | in.cram | |
| 1013 [ ... ] | |
| 1014 | |
| 1015 Quickly check that input files appear to be intact. Checks that beginning of the | |
| 1016 file contains a valid header (all formats) containing at least one target | |
| 1017 sequence and then seeks to the end of the file and checks that an end-of-file | |
| 1018 (EOF) is present and intact (BAM only). | |
| 1019 | |
| 1020 Data in the middle of the file is not read since that would be much more time | |
| 1021 consuming, so please note that this command will not detect internal corruption, | |
| 1022 but is useful for testing that files are not truncated before performing more | |
| 1023 intensive tasks on them. | |
| 1024 | |
| 1025 This command will exit with a non-zero exit code if any input files don't have a | |
| 1026 valid header or are missing an EOF block. Otherwise it will exit successfully | |
| 1027 (with a zero exit code). | |
| 1028 | |
| 1029 .B Options: | |
| 1030 .RS | |
| 1031 .TP 8 | |
| 1032 .B -v | |
| 1033 Verbose output: will additionally print the names of all input files that don't | |
| 1034 pass the check to stdout. Multiple -v options will cause additional messages | |
| 1035 regarding check results to be printed to stderr. | |
| 1036 .RE | |
| 1037 | |
| 1038 .TP \"-------- dict | |
| 1039 .B dict | |
| 1040 samtools dict <ref.fasta|ref.fasta.gz> | |
| 1041 | |
| 1042 Create a sequence dictionary file from a fasta file. | |
| 1043 | |
| 1044 .B OPTIONS: | |
| 1045 .RS | |
| 1046 .TP 11 | |
| 1047 .BI -a,\ --assembly \ STR | |
| 1048 Specify the assembly for the AS tag. | |
| 1049 .TP | |
| 1050 .B -H,\ --no-header | |
| 1051 Do not print the @HD header line. | |
| 1052 .TP | |
| 1053 .BI -o,\ --output \ FILE | |
| 1054 Output to | |
| 1055 .I FILE | |
| 1056 [stdout]. | |
| 1057 .TP | |
| 1058 .BI -s,\ --species \ STR | |
| 1059 Specify the species for the SP tag. | |
| 1060 .TP | |
| 1061 .BI -u,\ --uri \ STR | |
| 1062 Specify the URI for the UR tag. Defaults to | |
| 1063 the absolute path of | |
| 1064 .I ref.fasta | |
| 1065 unless reading from stdin. | |
| 1066 .RE | |
| 1067 | |
| 1068 .TP \"-------- fixmate | |
| 1069 .B fixmate | |
| 1070 .na | |
| 1071 samtools fixmate | |
| 1072 .RB [ -rpc ] | |
| 1073 .RB [ -O | |
| 1074 .IR format ] | |
| 1075 .I in.nameSrt.bam out.bam | |
| 1076 .ad | |
| 1077 | |
| 1078 Fill in mate coordinates, ISIZE and mate related flags from a | |
| 1079 name-sorted alignment. | |
| 1080 | |
| 1081 .B OPTIONS: | |
| 1082 .RS | |
| 1083 .TP 11 | |
| 1084 .B -r | |
| 1085 Remove secondary and unmapped reads. | |
| 1086 .TP | |
| 1087 .B -p | |
| 1088 Disable FR proper pair check. | |
| 1089 .TP | |
| 1090 .B -c | |
| 1091 Add template cigar ct tag. | |
| 1092 .TP | |
| 1093 .BI "-O " FORMAT | |
| 1094 Write the final output as | |
| 1095 .BR sam ", " bam ", or " cram . | |
| 1096 | |
| 1097 By default, samtools tries to select a format based on the output | |
| 1098 filename extension; if output is to standard output or no format can be | |
| 1099 deduced, | |
| 1100 .B bam | |
| 1101 is selected. | |
| 1102 .RE | |
| 1103 | |
| 1104 .TP \"-------- mpileup | |
| 1105 .B mpileup | |
| 1106 samtools mpileup | |
| 1107 .RB [ -EBugp ] | |
| 1108 .RB [ -C | |
| 1109 .IR capQcoef ] | |
| 1110 .RB [ -r | |
| 1111 .IR reg ] | |
| 1112 .RB [ -f | |
| 1113 .IR in.fa ] | |
| 1114 .RB [ -l | |
| 1115 .IR list ] | |
| 1116 .RB [ -Q | |
| 1117 .IR minBaseQ ] | |
| 1118 .RB [ -q | |
| 1119 .IR minMapQ ] | |
| 1120 .I in.bam | |
| 1121 .RI [ in2.bam | |
| 1122 .RI [ ... ]] | |
| 1123 | |
| 1124 Generate VCF, BCF or pileup for one or multiple BAM files. Alignment records | |
| 1125 are grouped by sample (SM) identifiers in @RG header lines. If sample | |
| 1126 identifiers are absent, each input file is regarded as one sample. | |
| 1127 | |
| 1128 In the pileup format (without | |
| 1129 .BR -u \ or \ -g ), | |
| 1130 each | |
| 1131 line represents a genomic position, consisting of chromosome name, | |
| 1132 1-based coordinate, reference base, the number of reads covering the site, | |
| 1133 read bases, base qualities and alignment | |
| 1134 mapping qualities. Information on match, mismatch, indel, strand, | |
| 1135 mapping quality and start and end of a read are all encoded at the read | |
| 1136 base column. At this column, a dot stands for a match to the reference | |
| 1137 base on the forward strand, a comma for a match on the reverse strand, | |
| 1138 a '>' or '<' for a reference skip, `ACGTN' for a mismatch on the forward | |
| 1139 strand and `acgtn' for a mismatch on the reverse strand. A pattern | |
| 1140 `\\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this | |
| 1141 reference position and the next reference position. The length of the | |
| 1142 insertion is given by the integer in the pattern, followed by the | |
| 1143 inserted sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+' | |
| 1144 represents a deletion from the reference. The deleted bases will be | |
| 1145 presented as `*' in the following lines. Also at the read base column, a | |
| 1146 symbol `^' marks the start of a read. The ASCII of the character | |
| 1147 following `^' minus 33 gives the mapping quality. A symbol `$' marks the | |
| 1148 end of a read segment. | |
| 1149 | |
| 1150 Note that there are two orthogonal ways to specify locations in the | |
| 1151 input file; via \fB-r\fR \fIregion\fR and \fB-l\fR \fIfile\fR. The | |
| 1152 former uses (and requires) an index to do random access while the | |
| 1153 latter streams through the file contents filtering out the specified | |
| 1154 regions, requiring no index. The two may be used in conjunction. For | |
| 1155 example a BED file containing locations of genes in chromosome 20 | |
| 1156 could be specified using \fB-r 20 -l chr20.bed\fR, meaning that the | |
| 1157 index is used to find chromosome 20 and then it is filtered for the | |
| 1158 regions listed in the bed file. | |
| 1159 | |
| 1160 .B Input Options: | |
| 1161 .RS | |
| 1162 .TP 10 | |
| 1163 .B -6, --illumina1.3+ | |
| 1164 Assume the quality is in the Illumina 1.3+ encoding. | |
| 1165 .TP | |
| 1166 .B -A, --count-orphans | |
| 1167 Do not skip anomalous read pairs in variant calling. | |
| 1168 .TP | |
| 1169 .BI -b,\ --bam-list \ FILE | |
| 1170 List of input BAM files, one file per line [null] | |
| 1171 .TP | |
| 1172 .B -B, --no-BAQ | |
| 1173 Disable probabilistic realignment for the computation of base alignment | |
| 1174 quality (BAQ). BAQ is the Phred-scaled probability of a read base being | |
| 1175 misaligned. Applying this option greatly helps to reduce false SNPs | |
| 1176 caused by misalignments. | |
| 1177 .TP | |
| 1178 .BI -C,\ --adjust-MQ \ INT | |
| 1179 Coefficient for downgrading mapping quality for reads containing | |
| 1180 excessive mismatches. Given a read with a phred-scaled probability q of | |
| 1181 being generated from the mapped position, the new mapping quality is | |
| 1182 about sqrt((INT-q)/INT)*INT. A zero value disables this | |
| 1183 functionality; if enabled, the recommended value for BWA is 50. [0] | |
| 1184 .TP | |
| 1185 .BI -d,\ --max-depth \ INT | |
| 1186 At a position, read maximally | |
| 1187 .I INT | |
| 1188 reads per input file. Note that samtools has a minimum value of | |
| 1189 .I 8000/n | |
| 1190 where | |
| 1191 .I n | |
| 1192 is the number of input files given to mpileup. This means the default | |
| 1193 is highly likely to be increased. Once above the cross-sample minimum of | |
| 1194 8000 the -d parameter will have an effect. [250] | |
| 1195 .TP | |
| 1196 .B -E, --redo-BAQ | |
| 1197 Recalculate BAQ on the fly, ignore existing BQ tags | |
| 1198 .TP | |
| 1199 .BI -f,\ --fasta-ref \ FILE | |
| 1200 The | |
| 1201 .BR faidx -indexed | |
| 1202 reference file in the FASTA format. The file can be optionally compressed by | |
| 1203 .BR bgzip . | |
| 1204 [null] | |
| 1205 .TP | |
| 1206 .BI -G,\ --exclude-RG \ FILE | |
| 1207 Exclude reads from readgroups listed in FILE (one @RG-ID per line) | |
| 1208 .TP | |
| 1209 .BI -l,\ --positions \ FILE | |
| 1210 BED or position list file containing a list of regions or sites where | |
| 1211 pileup or BCF should be generated. Position list files contain two | |
| 1212 columns (chromosome and position) and start counting from 1. BED | |
| 1213 files contain at least 3 columns (chromosome, start and end position) | |
| 1214 and are 0-based half-open. | |
| 1215 .br | |
| 1216 While it is possible to mix both position-list and BED coordinates in | |
| 1217 the same file, this is strongly ill advised due to the differing | |
| 1218 coordinate systems. [null] | |
| 1219 .TP | |
| 1220 .BI -q,\ -min-MQ \ INT | |
| 1221 Minimum mapping quality for an alignment to be used [0] | |
| 1222 .TP | |
| 1223 .BI -Q,\ --min-BQ \ INT | |
| 1224 Minimum base quality for a base to be considered [13] | |
| 1225 .TP | |
| 1226 .BI -r,\ --region \ STR | |
| 1227 Only generate pileup in region. Requires the BAM files to be indexed. | |
| 1228 If used in conjunction with -l then considers the intersection of the | |
| 1229 two requests. | |
| 1230 .I STR | |
| 1231 [all sites] | |
| 1232 .TP | |
| 1233 .B -R,\ --ignore-RG | |
| 1234 Ignore RG tags. Treat all reads in one BAM as one sample. | |
| 1235 .TP | |
| 1236 .BI --rf,\ --incl-flags \ STR|INT | |
| 1237 Required flags: skip reads with mask bits unset [null] | |
| 1238 .TP | |
| 1239 .BI --ff,\ --excl-flags \ STR|INT | |
| 1240 Filter flags: skip reads with mask bits set | |
| 1241 [UNMAP,SECONDARY,QCFAIL,DUP] | |
| 1242 .TP | |
| 1243 .B -x,\ --ignore-overlaps | |
| 1244 Disable read-pair overlap detection. | |
| 1245 .PP | |
| 1246 .B Output Options: | |
| 1247 .TP 10 | |
| 1248 .BI "-o, --output " FILE | |
| 1249 Write pileup or VCF/BCF output to | |
| 1250 .IR FILE , | |
| 1251 rather than the default of standard output. | |
| 1252 | |
| 1253 (The same short option is used for both | |
| 1254 .B --open-prob | |
| 1255 and | |
| 1256 .BR --output . | |
| 1257 If | |
| 1258 .BR -o 's | |
| 1259 argument contains any non-digit characters other than a leading + or - sign, | |
| 1260 it is interpreted as | |
| 1261 .BR --output . | |
| 1262 Usually the filename extension will take care of this, but to write to an | |
| 1263 entirely numeric filename use | |
| 1264 .B -o ./123 | |
| 1265 or | |
| 1266 .BR "--output 123" .) | |
| 1267 .TP | |
| 1268 .B -g,\ --BCF | |
| 1269 Compute genotype likelihoods and output them in the binary call format (BCF). | |
| 1270 As of v1.0, this is BCF2 which is incompatible with the BCF1 format produced | |
| 1271 by previous (0.1.x) versions of samtools. | |
| 1272 .TP | |
| 1273 .B -v,\ --VCF | |
| 1274 Compute genotype likelihoods and output them in the variant call format (VCF). | |
| 1275 Output is bgzip-compressed VCF unless | |
| 1276 .B -u | |
| 1277 option is set. | |
| 1278 .PP | |
| 1279 .B Output Options for mpileup format (without -g or -v): | |
| 1280 .TP 10 | |
| 1281 .B -O, --output-BP | |
| 1282 Output base positions on reads. | |
| 1283 .TP | |
| 1284 .B -s, --output-MQ | |
| 1285 Output mapping quality. | |
| 1286 .TP | |
| 1287 .B -a | |
| 1288 Output all positions, including those with zero depth. | |
| 1289 .TP | |
| 1290 .B -a -a, -aa | |
| 1291 Output absolutely all positions, including unused reference sequences. | |
| 1292 Note that when used in conjunction with a BED file the -a option may | |
| 1293 sometimes operate as if -aa was specified if the reference sequence | |
| 1294 has coverage outside of the region specified in the BED file. | |
| 1295 .PP | |
| 1296 .B Output Options for VCF/BCF format (with -g or -v): | |
| 1297 .TP 10 | |
| 1298 .B -D | |
| 1299 Output per-sample read depth [DEPRECATED - use | |
| 1300 .B -t DP | |
| 1301 instead] | |
| 1302 .TP | |
| 1303 .B -S | |
| 1304 Output per-sample Phred-scaled strand bias P-value [DEPRECATED - use | |
| 1305 .B -t SP | |
| 1306 instead] | |
| 1307 .TP | |
| 1308 .BI -t,\ --output-tags \ LIST | |
| 1309 Comma-separated list of FORMAT and INFO tags to output (case-insensitive): | |
| 1310 .B AD | |
| 1311 (Allelic depth, FORMAT), | |
| 1312 .B INFO/AD | |
| 1313 (Total allelic depth, INFO), | |
| 1314 .B ADF | |
| 1315 (Allelic depths on the forward strand, FORMAT), | |
| 1316 .B INFO/ADF | |
| 1317 (Total allelic depths on the forward strand, INFO), | |
| 1318 .B ADR | |
| 1319 (Allelic depths on the reverse strand, FORMAT), | |
| 1320 .B INFO/ADR | |
| 1321 (Total allelic depths on the reverse strand, INFO), | |
| 1322 .B DP | |
| 1323 (Number of high-quality bases, FORMAT), | |
| 1324 .B DV | |
| 1325 (Deprecated in favor of AD; Number of high-quality non-reference bases, FORMAT), | |
| 1326 .B DPR | |
| 1327 (Deprecated in favor of AD; Number of high-quality bases for each observed allele, FORMAT), | |
| 1328 .B INFO/DPR | |
| 1329 (Number of high-quality bases for each observed allele, INFO), | |
| 1330 .B DP4 | |
| 1331 (Deprecated in favor of ADF and ADR; Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases, FORMAT), | |
| 1332 .B SP | |
| 1333 (Phred-scaled strand bias P-value, FORMAT) | |
| 1334 [null] | |
| 1335 .TP | |
| 1336 .B -u,\ --uncompressed | |
| 1337 Generate uncompressed VCF/BCF output, which is preferred for piping. | |
| 1338 .TP | |
| 1339 .B -V | |
| 1340 Output per-sample number of non-reference reads [DEPRECATED - use | |
| 1341 .B -t DV | |
| 1342 instead] | |
| 1343 .PP | |
| 1344 .B Options for SNP/INDEL Genotype Likelihood Computation (for -g or -v): | |
| 1345 .TP 10 | |
| 1346 .BI -e,\ --ext-prob \ INT | |
| 1347 Phred-scaled gap extension sequencing error probability. Reducing | |
| 1348 .I INT | |
| 1349 leads to longer indels. [20] | |
| 1350 .TP | |
| 1351 .BI -F,\ --gap-frac \ FLOAT | |
| 1352 Minimum fraction of gapped reads [0.002] | |
| 1353 .TP | |
| 1354 .BI -h,\ --tandem-qual \ INT | |
| 1355 Coefficient for modeling homopolymer errors. Given an | |
| 1356 .IR l -long | |
| 1357 homopolymer | |
| 1358 run, the sequencing error of an indel of size | |
| 1359 .I s | |
| 1360 is modeled as | |
| 1361 .IR INT * s / l . | |
| 1362 [100] | |
| 1363 .TP | |
| 1364 .B -I, --skip-indels | |
| 1365 Do not perform INDEL calling | |
| 1366 .TP | |
| 1367 .BI -L,\ --max-idepth \ INT | |
| 1368 Skip INDEL calling if the average per-input-file depth is above | |
| 1369 .IR INT . | |
| 1370 [250] | |
| 1371 .TP | |
| 1372 .BI -m,\ --min-ireads \ INT | |
| 1373 Minimum number gapped reads for indel candidates | |
| 1374 .IR INT . | |
| 1375 [1] | |
| 1376 .TP | |
| 1377 .BI -o,\ --open-prob \ INT | |
| 1378 Phred-scaled gap open sequencing error probability. Reducing | |
| 1379 .I INT | |
| 1380 leads to more indel calls. [40] | |
| 1381 | |
| 1382 (The same short option is used for both | |
| 1383 .B --open-prob | |
| 1384 and | |
| 1385 .BR --output . | |
| 1386 When | |
| 1387 .BR -o 's | |
| 1388 argument contains only an optional + or - sign followed by the digits 0 to 9, | |
| 1389 it is interpreted as | |
| 1390 .BR --open-prob .) | |
| 1391 .TP | |
| 1392 .B -p, --per-sample-mF | |
| 1393 Apply | |
| 1394 .B -m | |
| 1395 and | |
| 1396 .B -F | |
| 1397 thresholds per sample to increase sensitivity of calling. | |
| 1398 By default both options are applied to reads pooled from all samples. | |
| 1399 .TP | |
| 1400 .BI -P,\ --platforms \ STR | |
| 1401 Comma-delimited list of platforms (determined by | |
| 1402 .BR @RG-PL ) | |
| 1403 from which indel candidates are obtained. It is recommended to collect | |
| 1404 indel candidates from sequencing technologies that have low indel error | |
| 1405 rate such as ILLUMINA. [all] | |
| 1406 .RE | |
| 1407 | |
| 1408 .TP \"-------- flags | |
| 1409 .B flags | |
| 1410 samtools flags INT|STR[,...] | |
| 1411 | |
| 1412 Convert between textual and numeric flag representation. | |
| 1413 | |
| 1414 .B FLAGS: | |
| 1415 .TS | |
| 1416 rb l l . | |
| 1417 0x1 PAIRED paired-end (or multiple-segment) sequencing technology | |
| 1418 0x2 PROPER_PAIR each segment properly aligned according to the aligner | |
| 1419 0x4 UNMAP segment unmapped | |
| 1420 0x8 MUNMAP next segment in the template unmapped | |
| 1421 0x10 REVERSE SEQ is reverse complemented | |
| 1422 0x20 MREVERSE SEQ of the next segment in the template is reverse complemented | |
| 1423 0x40 READ1 the first segment in the template | |
| 1424 0x80 READ2 the last segment in the template | |
| 1425 0x100 SECONDARY secondary alignment | |
| 1426 0x200 QCFAIL not passing quality controls | |
| 1427 0x400 DUP PCR or optical duplicate | |
| 1428 0x800 SUPPLEMENTARY supplementary alignment | |
| 1429 .TE | |
| 1430 | |
| 1431 .TP \"-------- fastq fasta | |
| 1432 .B fastq/a | |
| 1433 samtools fastq | |
| 1434 .RI [ options ] | |
| 1435 .I in.bam | |
| 1436 .br | |
| 1437 samtools fasta | |
| 1438 .RI [ options ] | |
| 1439 .I in.bam | |
| 1440 | |
| 1441 Converts a BAM or CRAM into either FASTQ or FASTA format depending on the | |
| 1442 command invoked. The FASTQ files will be automatically compressed if the | |
| 1443 filenames have a .gz or .bgzf extention. | |
| 1444 | |
| 1445 .B OPTIONS: | |
| 1446 .RS | |
| 1447 .TP 8 | |
| 1448 .B -n | |
| 1449 By default, either '/1' or '/2' is added to the end of read names | |
| 1450 where the corresponding BAM_READ1 or BAM_READ2 flag is set. | |
| 1451 Using | |
| 1452 .B -n | |
| 1453 causes read names to be left as they are. | |
| 1454 .TP 8 | |
| 1455 .B -N | |
| 1456 Always add either '/1' or '/2' to the end of read names | |
| 1457 even when put into different files. | |
| 1458 .TP 8 | |
| 1459 .B -O | |
| 1460 Use quality values from OQ tags in preference to standard quality string | |
| 1461 if available. | |
| 1462 .TP 8 | |
| 1463 .B -s FILE | |
| 1464 Write singleton reads in FASTQ format to FILE instead of outputting them. | |
| 1465 .TP 8 | |
| 1466 .B -t | |
| 1467 Copy RG, BC and QT tags to the FASTQ header line, if they exist. | |
| 1468 .TP 8 | |
| 1469 .B -T TAGLIST | |
| 1470 Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist. | |
| 1471 .TP 8 | |
| 1472 .B -1 FILE | |
| 1473 Write reads with the BAM_READ1 flag set to FILE instead of outputting them. | |
| 1474 .TP 8 | |
| 1475 .B -2 FILE | |
| 1476 Write reads with the BAM_READ2 flag set to FILE instead of outputting them. | |
| 1477 .TP 8 | |
| 1478 .B -0 FILE | |
| 1479 Write reads with both or neither of the BAM_READ1 and BAM_READ2 flags set | |
| 1480 to FILE instead of outputting them. | |
| 1481 .TP 8 | |
| 1482 .BI "-f " INT | |
| 1483 Only output alignments with all bits set in | |
| 1484 .I INT | |
| 1485 present in the FLAG field. | |
| 1486 .I INT | |
| 1487 can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) | |
| 1488 or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]. | |
| 1489 .TP 8 | |
| 1490 .BI "-F " INT | |
| 1491 Do not output alignments with any bits set in | |
| 1492 .I INT | |
| 1493 present in the FLAG field. | |
| 1494 .I INT | |
| 1495 can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) | |
| 1496 or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]. | |
| 1497 .TP 8 | |
| 1498 .BI "-G " INT | |
| 1499 Only EXCLUDE reads with all of the bits set in | |
| 1500 .I INT | |
| 1501 present in the FLAG field. | |
| 1502 .I INT | |
| 1503 can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) | |
| 1504 or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]. | |
| 1505 .TP 8 | |
| 1506 .B -i | |
| 1507 add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG) | |
| 1508 .TP 8 | |
| 1509 .B -c [0..9] | |
| 1510 set compression level when writing gz or bgzf fastq files. | |
| 1511 .TP 8 | |
| 1512 .B --i1 FILE | |
| 1513 write first index reads to FILE | |
| 1514 .TP 8 | |
| 1515 .B --i2 FILE | |
| 1516 write second index reads to FILE | |
| 1517 .TP 8 | |
| 1518 .B --barcode-tag TAG | |
| 1519 aux tag to find index reads in [default: BC] | |
| 1520 .TP 8 | |
| 1521 .B --quality-tag TAG | |
| 1522 aux tag to find index quality in [default: QT] | |
| 1523 .TP 8 | |
| 1524 .B --index-format STR | |
| 1525 string to describe how to parse the barcode and quality tags. For example: | |
| 1526 | |
| 1527 .RS | |
| 1528 .TP 8 | |
| 1529 .B i14i8 | |
| 1530 the first 14 characters are index 1, the next 8 characters are index 2 | |
| 1531 .TP 8 | |
| 1532 .B n8i14 | |
| 1533 ignore the first 8 characters, and use the next 14 characters for index 1 | |
| 1534 | |
| 1535 If the tag contains a separator, then the numeric part can be replaced with '*' to | |
| 1536 mean 'read until the separator or end of tag', for example: | |
| 1537 .TP 8 | |
| 1538 .B n*i* | |
| 1539 ignore the left part of the tag until the separator, then use the second part | |
| 1540 .RE | |
| 1541 .RE | |
| 1542 | |
| 1543 .TP \"-------- collate | |
| 1544 .B collate | |
| 1545 samtools collate | |
| 1546 .RI [ options ] | |
| 1547 .IR in.sam | in.bam | in.cram " [" out.prefix "]" | |
| 1548 | |
| 1549 Shuffles and groups reads together by their names. | |
| 1550 A faster alternative to a full query name sort, | |
| 1551 .B collate | |
| 1552 ensures that reads of the same name are grouped together in contiguous groups, | |
| 1553 but doesn't make any guarantees about the order of read names between groups. | |
| 1554 | |
| 1555 The output from this command should be suitable for any operation that | |
| 1556 requires all reads from the same template to be grouped together. | |
| 1557 | |
| 1558 .B Options: | |
| 1559 .RS | |
| 1560 .TP 8 | |
| 1561 .B -O | |
| 1562 Output to stdout rather than to files starting with out.prefix | |
| 1563 .TP | |
| 1564 .B -u | |
| 1565 Write uncompressed BAM output | |
| 1566 .TP | |
| 1567 .BI "-l " INT | |
| 1568 Compression level. | |
| 1569 [1] | |
| 1570 .TP | |
| 1571 .BI "-n " INT | |
| 1572 Number of temporary files to use. | |
| 1573 [64] | |
| 1574 .RE | |
| 1575 | |
| 1576 .TP \"-------- reheader | |
| 1577 .B reheader | |
| 1578 samtools reheader | |
| 1579 .RB [ -iP ] | |
| 1580 .I in.header.sam in.bam | |
| 1581 | |
| 1582 Replace the header in | |
| 1583 .I in.bam | |
| 1584 with the header in | |
| 1585 .IR in.header.sam . | |
| 1586 This command is much faster than replacing the header with a | |
| 1587 BAM\(->SAM\(->BAM conversion. | |
| 1588 | |
| 1589 By default this command outputs the BAM or CRAM file to standard | |
| 1590 output (stdout), but for CRAM format files it has the option to | |
| 1591 perform an in-place edit, both reading and writing to the same file. | |
| 1592 No validity checking is performed on the header, nor that it is suitable | |
| 1593 to use with the sequence data itself. | |
| 1594 | |
| 1595 .B OPTIONS: | |
| 1596 .RS | |
| 1597 .TP 8 | |
| 1598 .B -P, --no-PG | |
| 1599 Do not generate an @PG header line. | |
| 1600 .TP 8 | |
| 1601 .B -i, --in-place | |
| 1602 Perform the header edit in-place, if possible. This only works on CRAM | |
| 1603 files and only if there is sufficient room to store the new header. | |
| 1604 The amount of space available will differ for each CRAM file. | |
| 1605 .RE | |
| 1606 | |
| 1607 .TP \"-------- cat | |
| 1608 .B cat | |
| 1609 samtools cat [-b list] [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ] | |
| 1610 | |
| 1611 Concatenate BAMs or CRAMs. Although this works on either BAM or CRAM, | |
| 1612 all input files must be the same format as each other. The sequence | |
| 1613 dictionary of each input file must be identical, although this command | |
| 1614 does not check this. This command uses a similar trick to | |
| 1615 .B reheader | |
| 1616 which enables fast BAM concatenation. | |
| 1617 | |
| 1618 .B OPTIONS: | |
| 1619 .RS | |
| 1620 .TP 8 | |
| 1621 .BI "-b " FOFN | |
| 1622 Read the list of input BAM or CRAM files from \fIFOFN\fR. These are | |
| 1623 concatenated prior to any files specified on the command line. | |
| 1624 Multiple \fB-b\fR \fIFOFN\fR options may be specified to concatenate | |
| 1625 multiple lists of BAM/CRAM files. | |
| 1626 .TP 8 | |
| 1627 .BI "-h " FILE | |
| 1628 Uses the SAM header from \fIFILE\fR. By default the header is taken | |
| 1629 from the first file to be concatenated. | |
| 1630 .TP 8 | |
| 1631 .BI "-o " FILE | |
| 1632 Write the concatenated output to \fIFILE\fR. By default this is sent | |
| 1633 to stdout. | |
| 1634 .RE | |
| 1635 | |
| 1636 .TP \"-------- rmdup | |
| 1637 .B rmdup | |
| 1638 samtools rmdup [-sS] <input.srt.bam> <out.bam> | |
| 1639 | |
| 1640 Remove potential PCR duplicates: if multiple read pairs have identical | |
| 1641 external coordinates, only retain the pair with highest mapping quality. | |
| 1642 In the paired-end mode, this command | |
| 1643 .B ONLY | |
| 1644 works with FR orientation and requires ISIZE is correctly set. It does | |
| 1645 not work for unpaired reads (e.g. two ends mapped to different | |
| 1646 chromosomes or orphan reads). | |
| 1647 | |
| 1648 .B OPTIONS: | |
| 1649 .RS | |
| 1650 .TP 8 | |
| 1651 .B -s | |
| 1652 Remove duplicates for single-end reads. By default, the command works for | |
| 1653 paired-end reads only. | |
| 1654 .TP 8 | |
| 1655 .B -S | |
| 1656 Treat paired-end reads and single-end reads. | |
| 1657 .RE | |
| 1658 | |
| 1659 .TP \"-------- addreplacerg | |
| 1660 .B addreplacerg | |
| 1661 samtools addreplacerg [-r rg line | -R rg ID] [-m mode] [-l level] [-o out.bam] | |
| 1662 <input.bam> | |
| 1663 | |
| 1664 Adds or replaces read group tags in a file. | |
| 1665 | |
| 1666 .B OPTIONS: | |
| 1667 .RS | |
| 1668 .TP 8 | |
| 1669 .BI "-r " STRING | |
| 1670 Allows you to specify a read group line to append to the header and applies it | |
| 1671 to the reads specified by the -m option. If repeated it automatically adds in | |
| 1672 tabs between invocations. | |
| 1673 .TP 8 | |
| 1674 .BI "-R " STRING | |
| 1675 Allows you to specify the read group ID of an existing @RG line and applies it | |
| 1676 to the reads specified. | |
| 1677 .TP 8 | |
| 1678 .BI "-m " MODE | |
| 1679 If you choose orphan_only then existing RG tags are not overwritten, if you choose | |
| 1680 overwrite_all, existing RG tags are overwritten. The default is overwrite_all. | |
| 1681 .TP 8 | |
| 1682 .BI "-o " STRING | |
| 1683 Write the final output to STRING. The default is to write to stdout. | |
| 1684 | |
| 1685 By default, samtools tries to select a format based on the output | |
| 1686 filename extension; if output is to standard output or no format can be | |
| 1687 deduced, | |
| 1688 .B bam | |
| 1689 is selected. | |
| 1690 .RE | |
| 1691 | |
| 1692 .TP \"-------- calmd | |
| 1693 .B calmd | |
| 1694 samtools calmd [-Eeubr] [-C capQcoef] <aln.bam> <ref.fasta> | |
| 1695 | |
| 1696 Generate the MD tag. If the MD tag is already present, this command will | |
| 1697 give a warning if the MD tag generated is different from the existing | |
| 1698 tag. Output SAM by default. | |
| 1699 | |
| 1700 Calmd can also read and write CRAM files although in most cases it is | |
| 1701 pointless as CRAM recalculates MD and NM tags on the fly. The one | |
| 1702 exception to this case is where both input and output CRAM files | |
| 1703 have been / are being created with the \fIno_ref\fR option. | |
| 1704 | |
| 1705 .B OPTIONS: | |
| 1706 .RS | |
| 1707 .TP 8 | |
| 1708 .B -A | |
| 1709 When used jointly with | |
| 1710 .B -r | |
| 1711 this option overwrites the original base quality. | |
| 1712 .TP 8 | |
| 1713 .B -e | |
| 1714 Convert a the read base to = if it is identical to the aligned reference | |
| 1715 base. Indel caller does not support the = bases at the moment. | |
| 1716 .TP | |
| 1717 .B -u | |
| 1718 Output uncompressed BAM | |
| 1719 .TP | |
| 1720 .B -b | |
| 1721 Output compressed BAM | |
| 1722 .TP | |
| 1723 .BI -C \ INT | |
| 1724 Coefficient to cap mapping quality of poorly mapped reads. See the | |
| 1725 .B pileup | |
| 1726 command for details. [0] | |
| 1727 .TP | |
| 1728 .B -r | |
| 1729 Compute the BQ tag (without -A) or cap base quality by BAQ (with -A). | |
| 1730 .TP | |
| 1731 .B -E | |
| 1732 Extended BAQ calculation. This option trades specificity for sensitivity, though the | |
| 1733 effect is minor. | |
| 1734 .RE | |
| 1735 | |
| 1736 .TP \"-------- targetcut | |
| 1737 .B targetcut | |
| 1738 samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam> | |
| 1739 | |
| 1740 This command identifies target regions by examining the continuity of read depth, computes | |
| 1741 haploid consensus sequences of targets and outputs a SAM with each sequence corresponding | |
| 1742 to a target. When option | |
| 1743 .B -f | |
| 1744 is in use, BAQ will be applied. This command is | |
| 1745 .B only | |
| 1746 designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et al. (2010)]. | |
| 1747 | |
| 1748 .TP \"-------- phase | |
| 1749 .B phase | |
| 1750 samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam> | |
| 1751 | |
| 1752 Call and phase heterozygous SNPs. | |
| 1753 | |
| 1754 .B OPTIONS: | |
| 1755 .RS | |
| 1756 .TP 8 | |
| 1757 .B -A | |
| 1758 Drop reads with ambiguous phase. | |
| 1759 .TP 8 | |
| 1760 .BI -b \ STR | |
| 1761 Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file | |
| 1762 .BR STR .0.bam | |
| 1763 and phase-1 reads in | |
| 1764 .BR STR .1.bam. | |
| 1765 Phase unknown reads will be randomly allocated to one of the two files. Chimeric reads | |
| 1766 with switch errors will be saved in | |
| 1767 .BR STR .chimeric.bam. | |
| 1768 [null] | |
| 1769 .TP | |
| 1770 .B -F | |
| 1771 Do not attempt to fix chimeric reads. | |
| 1772 .TP | |
| 1773 .BI -k \ INT | |
| 1774 Maximum length for local phasing. [13] | |
| 1775 .TP | |
| 1776 .BI -q \ INT | |
| 1777 Minimum Phred-scaled LOD to call a heterozygote. [40] | |
| 1778 .TP | |
| 1779 .BI -Q \ INT | |
| 1780 Minimum base quality to be used in het calling. [13] | |
| 1781 .RE | |
| 1782 | |
| 1783 .TP \"-------- depad | |
| 1784 .B depad | |
| 1785 samtools depad [-SsCu1] [-T ref.fa] [-o output] <in.bam> | |
| 1786 | |
| 1787 Converts a BAM aligned against a padded reference to a BAM aligned | |
| 1788 against the depadded reference. The padded reference may contain | |
| 1789 verbatim "*" bases in it, but "*" bases are also counted in the | |
| 1790 reference numbering. This means that a sequence base-call aligned | |
| 1791 against a reference "*" is considered to be a cigar match ("M" or "X") | |
| 1792 operator (if the base-call is "A", "C", "G" or "T"). After depadding | |
| 1793 the reference "*" bases are deleted and such aligned sequence | |
| 1794 base-calls become insertions. Similarly transformations apply for | |
| 1795 deletions and padding cigar operations. | |
| 1796 | |
| 1797 .B OPTIONS: | |
| 1798 .RS | |
| 1799 .TP | |
| 1800 .B -S | |
| 1801 Ignored for compatibility with previous samtools versions. | |
| 1802 Previously this option was required if input was in SAM format, but now the | |
| 1803 correct format is automatically detected by examining the first few characters | |
| 1804 of input. | |
| 1805 .TP | |
| 1806 .B -s | |
| 1807 Output in SAM format. The default is BAM. | |
| 1808 .TP | |
| 1809 .B -C | |
| 1810 Output in CRAM format. The default is BAM. | |
| 1811 .TP | |
| 1812 .B -u | |
| 1813 Do not compress the output. Applies to either BAM or CRAM output | |
| 1814 format. | |
| 1815 .TP | |
| 1816 .B -1 | |
| 1817 Enable fastest compression level. Only works for BAM or CRAM output. | |
| 1818 .TP | |
| 1819 .BI "-T " FILE | |
| 1820 Provides the padded reference file. Note that without this the @SQ | |
| 1821 line lengths will be incorrect, so for most use cases this option will | |
| 1822 be considered as mandatory. | |
| 1823 .TP | |
| 1824 .BI "-o " FILE | |
| 1825 Specifies the output filename. By default output is sent to stdout. | |
| 1826 .RE | |
| 1827 | |
| 1828 .TP \"-------- help etc | |
| 1829 .BR help ,\ --help | |
| 1830 Display a brief usage message listing the samtools commands available. | |
| 1831 If the name of a command is also given, e.g., | |
| 1832 .BR samtools\ help\ view , | |
| 1833 the detailed usage message for that particular command is displayed. | |
| 1834 | |
| 1835 .TP | |
| 1836 .B --version | |
| 1837 Display the version numbers and copyright information for samtools and | |
| 1838 the important libraries used by samtools. | |
| 1839 | |
| 1840 .TP | |
| 1841 .B --version-only | |
| 1842 Display the full samtools version number in a machine-readable format. | |
| 1843 .PP | |
| 1844 .SH GLOBAL OPTIONS | |
| 1845 .PP | |
| 1846 Several long-options are shared between multiple samtools subcommands: | |
| 1847 \fB--input-fmt\fR, \fB--input-fmt-options\fR, \fB--output-fmt\fR, | |
| 1848 \fB--output-fmt-options\fR, and \fB--reference\fR. | |
| 1849 The input format is typically auto-detected so specifying the format | |
| 1850 is usually unnecessary and the option is included for completeness. | |
| 1851 Note that not all subcommands have all options. Consult the subcommand | |
| 1852 help for more details. | |
| 1853 .PP | |
| 1854 Format strings recognised are "sam", "bam" and "cram". They may be | |
| 1855 followed by a comma separated list of options as \fIkey\fR or | |
| 1856 \fIkey\fR=\fIvalue\fR. See below for examples. | |
| 1857 .PP | |
| 1858 The \fBfmt-options\fR arguments accept either a single \fIoption\fR or | |
| 1859 \fIoption\fR=\fIvalue\fR. Note that some options only work on some | |
| 1860 file formats and only on read or write streams. If value is | |
| 1861 unspecified for a boolean option, the value is assumed to be 1. The | |
| 1862 valid options are as follows. | |
| 1863 .RS 0 | |
| 1864 .\" General purpose | |
| 1865 .TP 4 | |
| 1866 .BI nthreads= INT | |
| 1867 Specifies the number of threads to use during encoding and/or | |
| 1868 decoding. For BAM this will be encoding only. In CRAM the threads | |
| 1869 are dynamically shared between encoder and decoder. | |
| 1870 .\" CRAM specific | |
| 1871 .TP | |
| 1872 .BI reference= fasta_file | |
| 1873 Specifies a FASTA reference file for use in CRAM encoding or decoding. | |
| 1874 It usually is not required for decoding except in the situation of the | |
| 1875 MD5 not being obtainable via the REF_PATH or REF_CACHE environment variables. | |
| 1876 .TP | |
| 1877 .BI decode_md= 0|1 | |
| 1878 CRAM input only; defaults to 1 (on). CRAM does not typically store | |
| 1879 MD and NM tags, preferring to generate them on the fly. This option | |
| 1880 controls this behaviour. | |
| 1881 .TP | |
| 1882 .BI ignore_md5= 0|1 | |
| 1883 CRAM input only; defaults to 0 (off). When enabled, md5 checksum | |
| 1884 errors on the reference sequence and block checksum errors within CRAM | |
| 1885 are ignored. Use of this option is strongly discouraged. | |
| 1886 .TP | |
| 1887 .BI required_fields= bit-field | |
| 1888 CRAM input only; specifies which SAM columns need to be populated. | |
| 1889 By default all fields are used. Limiting the decode to specific | |
| 1890 columns can have significant performance gains. The bit-field is a | |
| 1891 numerical value constructed from the following table. | |
| 1892 .TS | |
| 1893 center; | |
| 1894 rb l . | |
| 1895 0x1 SAM_QNAME | |
| 1896 0x2 SAM_FLAG | |
| 1897 0x4 SAM_RNAME | |
| 1898 0x8 SAM_POS | |
| 1899 0x10 SAM_MAPQ | |
| 1900 0x20 SAM_CIGAR | |
| 1901 0x40 SAM_RNEXT | |
| 1902 0x80 SAM_PNEXT | |
| 1903 0x100 SAM_TLEN | |
| 1904 0x200 SAM_SEQ | |
| 1905 0x400 SAM_QUAL | |
| 1906 0x800 SAM_AUX | |
| 1907 0x1000 SAM_RGAUX | |
| 1908 .TE | |
| 1909 .TP | |
| 1910 .BI name_prefix= string | |
| 1911 CRAM input only; defaults to output filename. Any sequences with | |
| 1912 auto-generated read names will use \fIstring\fR as the name prefix. | |
| 1913 .TP | |
| 1914 .BI multi_seq_per_slice= 0|1 | |
| 1915 CRAM output only; defaults to 0 (off). By default CRAM generates one | |
| 1916 container per reference sequence, except in the case of many small | |
| 1917 references (such as a fragmented assembly). | |
| 1918 .TP | |
| 1919 .BI version= major.minor | |
| 1920 CRAM output only. Specifies the CRAM version number. Acceptable | |
| 1921 values are "2.1" and "3.0". | |
| 1922 .TP | |
| 1923 .BI seqs_per_slice= INT | |
| 1924 CRAM output only; defaults to 10000. | |
| 1925 .TP | |
| 1926 .BI slices_per_container= INT | |
| 1927 CRAM output only; defaults to 1. The effect of having multiple slices | |
| 1928 per container is to share the compression header block between | |
| 1929 multiple slices. This is unlikely to have any significant impact | |
| 1930 unless the number of sequences per slice is reduced. (Together these | |
| 1931 two options control the granularity of random access.) | |
| 1932 .TP | |
| 1933 .BI embed_ref= 0|1 | |
| 1934 CRAM output only; defaults to 0 (off). If 1, this will store portions | |
| 1935 of the reference sequence in each slice, permitting decode without | |
| 1936 having requiring an external copy of the reference sequence. | |
| 1937 .TP | |
| 1938 .BI no_ref= 0|1 | |
| 1939 CRAM output only; defaults to 0 (off). If 1, sequences will be stored | |
| 1940 verbatim with no reference encoding. This can be useful if no | |
| 1941 reference is available for the file. | |
| 1942 .TP | |
| 1943 .BI use_bzip2= 0|1 | |
| 1944 CRAM output only; defaults to 0 (off). Permits use of bzip2 in CRAM | |
| 1945 block compression. | |
| 1946 .TP | |
| 1947 .BI use_lzma= 0|1 | |
| 1948 CRAM output only; defaults to 0 (off). Permits use of lzma in CRAM | |
| 1949 block compression. | |
| 1950 .TP | |
| 1951 .BI lossy_names= 0|1 | |
| 1952 CRAM output only; defaults to 0 (off). If 1, templates with all | |
| 1953 members within the same CRAM slice will have their read names | |
| 1954 removed. New names will be automatically generated during decoding. | |
| 1955 Also see the \fBname_prefix\fR option. | |
| 1956 .RE | |
| 1957 .PP | |
| 1958 For example: | |
| 1959 .EX 4 | |
| 1960 samtools view --input-fmt-option decode_md=0 | |
| 1961 --output-fmt cram,version=3.0 --output-fmt-option embed_ref | |
| 1962 --output-fmt-option seqs_per_slice=2000 -o foo.cram foo.bam | |
| 1963 .EE | |
| 1964 .PP | |
| 1965 .SH REFERENCE SEQUENCES | |
| 1966 .PP | |
| 1967 The CRAM format requires use of a reference sequence for both reading | |
| 1968 and writing. | |
| 1969 .PP | |
| 1970 When reading a CRAM the \fB@SQ\fR headers are interrogated to identify | |
| 1971 the reference sequence MD5sum (\fBM5:\fR tag) and the local reference | |
| 1972 sequence filename (\fBUR:\fR tag). Note that \fIhttp://\fR and | |
| 1973 \fIftp://\fR based URLs in the UR: field are not used, but local fasta | |
| 1974 filenames (with or without \fIfile://\fR) can be used. | |
| 1975 .PP | |
| 1976 To create a CRAM the \fB@SQ\fR headers will also be read to identify | |
| 1977 the reference sequences, but M5: and UR: tags may not be present. In | |
| 1978 this case the \fB-T\fR and \fB-t\fR options of samtools view may be | |
| 1979 used to specify the fasta or fasta.fai filenames respectively | |
| 1980 (provided the .fasta.fai file is also backed up by a .fasta file). | |
| 1981 .PP | |
| 1982 The search order to obtain a reference is: | |
| 1983 .IP 1. 3 | |
| 1984 Use any local file specified by the command line options (eg -T). | |
| 1985 .IP 2. 3 | |
| 1986 Look for MD5 via REF_CACHE environment variable. | |
| 1987 .IP 3. 3 | |
| 1988 Look for MD5 in each element of the REF_PATH environment variable. | |
| 1989 .IP 4. 3 | |
| 1990 Look for a local file listed in the UR: header tag. | |
| 1991 .PP | |
| 1992 .SH ENVIRONMENT VARIABLES | |
| 1993 .PP | |
| 1994 .TP | |
| 1995 .B HTS_PATH | |
| 1996 A colon-separated list of directories in which to search for HTSlib plugins. | |
| 1997 If $HTS_PATH starts or ends with a colon or contains a double colon (\fB::\fP), | |
| 1998 the built-in list of directories is searched at that point in the search. | |
| 1999 | |
| 2000 If no HTS_PATH variable is defined, the built-in list of directories | |
| 2001 specified when HTSlib was built is used, which typically includes | |
| 2002 \fB/usr/local/libexec/htslib\fP and similar directories. | |
| 2003 | |
| 2004 .TP | |
| 2005 .B REF_PATH | |
| 2006 A colon separated (semi-colon on Windows) list of locations in which | |
| 2007 to look for sequences identified by their MD5sums. This can be either | |
| 2008 a list of directories or URLs. Note that if a URL is included then the | |
| 2009 colon in http:// and ftp:// and the optional port number will be | |
| 2010 treated as part of the URL and not a PATH field separator. | |
| 2011 For URLs, the text \fB%s\fR will be replaced by the MD5sum being | |
| 2012 read. | |
| 2013 | |
| 2014 If no REF_PATH has been specified it will default to | |
| 2015 \fBhttp://www.ebi.ac.uk/ena/cram/md5/%s\fR and if REF_CACHE is also unset, | |
| 2016 it will be set to \fB$XDG_CACHE_HOME/hts-ref/%2s/%2s/%s\fR. | |
| 2017 If \fB$XDG_CACHE_HOME\fR is unset, \fB$HOME/.cache\fR (or a local system | |
| 2018 temporary directory if no home directory is found) will be used similarly. | |
| 2019 | |
| 2020 .TP | |
| 2021 .B REF_CACHE | |
| 2022 This can be defined to a single directory housing a local cache of | |
| 2023 references. Upon downloading a reference it will be stored in the | |
| 2024 location pointed to by REF_CACHE. When reading a reference it will be | |
| 2025 looked for in this directory before searching REF_PATH. To avoid many | |
| 2026 files being stored in the same directory, a pathname may be | |
| 2027 constructed using %\fInum\fRs and %s notation, consuming \fInum\fR | |
| 2028 characters of the MD5sum. For example | |
| 2029 \fB/local/ref_cache/%2s/%2s/%s\fR will create 2 nested subdirectories | |
| 2030 with the filenames in the deepest directory being the last 28 | |
| 2031 characters of the md5sum. | |
| 2032 | |
| 2033 The REF_CACHE directory will be searched for before attempting to load | |
| 2034 via the REF_PATH search list. If no REF_PATH is defined, both | |
| 2035 REF_PATH and REF_CACHE will be automatically set (see above), but if | |
| 2036 REF_PATH is defined and REF_CACHE not then no local cache is used. | |
| 2037 | |
| 2038 To aid population of the REF_CACHE directory a script | |
| 2039 \fBmisc/seq_cache_populate.pl\fR is provided in the Samtools | |
| 2040 distribution. This takes a fasta file or a directory of fasta files | |
| 2041 and generates the MD5sum named files. | |
| 2042 .PP | |
| 2043 .SH EXAMPLES | |
| 2044 .IP o 2 | |
| 2045 Import SAM to BAM when | |
| 2046 .B @SQ | |
| 2047 lines are present in the header: | |
| 2048 .EX 2 | |
| 2049 samtools view -bS aln.sam > aln.bam | |
| 2050 .EE | |
| 2051 If | |
| 2052 .B @SQ | |
| 2053 lines are absent: | |
| 2054 .EX 2 | |
| 2055 samtools faidx ref.fa | |
| 2056 samtools view -bt ref.fa.fai aln.sam > aln.bam | |
| 2057 .EE | |
| 2058 where | |
| 2059 .I ref.fa.fai | |
| 2060 is generated automatically by the | |
| 2061 .B faidx | |
| 2062 command. | |
| 2063 | |
| 2064 .IP o 2 | |
| 2065 Convert a BAM file to a CRAM file using a local reference sequence. | |
| 2066 .EX 2 | |
| 2067 samtools view -C -T ref.fa aln.bam > aln.cram | |
| 2068 .EE | |
| 2069 .IP o 2 | |
| 2070 Attach the | |
| 2071 .B RG | |
| 2072 tag while merging sorted alignments: | |
| 2073 .EX 2 | |
| 2074 perl -e 'print "@RG\\tID:ga\\tSM:hs\\tLB:ga\\tPL:Illumina\\n@RG\\tID:454\\tSM:hs\\tLB:454\\tPL:454\\n"' > rg.txt | |
| 2075 samtools merge -rh rg.txt merged.bam ga.bam 454.bam | |
| 2076 .EE | |
| 2077 The value in a | |
| 2078 .B RG | |
| 2079 tag is determined by the file name the read is coming from. In this | |
| 2080 example, in the | |
| 2081 .IR merged.bam , | |
| 2082 reads from | |
| 2083 .I ga.bam | |
| 2084 will be attached | |
| 2085 .IR RG:Z:ga , | |
| 2086 while reads from | |
| 2087 .I 454.bam | |
| 2088 will be attached | |
| 2089 .IR RG:Z:454 . | |
| 2090 | |
| 2091 .IP o 2 | |
| 2092 Call SNPs and short INDELs: | |
| 2093 .EX 2 | |
| 2094 samtools mpileup -uf ref.fa aln.bam | bcftools call -mv > var.raw.vcf | |
| 2095 bcftools filter -s LowQual -e '%QUAL<20 || DP>100' var.raw.vcf > var.flt.vcf | |
| 2096 .EE | |
| 2097 The | |
| 2098 .B bcftools filter | |
| 2099 command marks low quality sites and sites with the read depth exceeding | |
| 2100 a limit, which should be adjusted to about twice the average read depth | |
| 2101 (bigger read depths usually indicate problematic regions which are | |
| 2102 often enriched for artefacts). One may consider to add | |
| 2103 .B -C50 | |
| 2104 to | |
| 2105 .B mpileup | |
| 2106 if mapping quality is overestimated for reads containing excessive | |
| 2107 mismatches. Applying this option usually helps | |
| 2108 .B BWA-short | |
| 2109 but may not other mappers. | |
| 2110 | |
| 2111 Individuals are identified from the | |
| 2112 .B SM | |
| 2113 tags in the | |
| 2114 .B @RG | |
| 2115 header lines. Individuals can be pooled in one alignment file; one | |
| 2116 individual can also be separated into multiple files. The | |
| 2117 .B -P | |
| 2118 option specifies that indel candidates should be collected only from | |
| 2119 read groups with the | |
| 2120 .B @RG-PL | |
| 2121 tag set to | |
| 2122 .IR ILLUMINA . | |
| 2123 Collecting indel candidates from reads sequenced by an indel-prone | |
| 2124 technology may affect the performance of indel calling. | |
| 2125 | |
| 2126 .IP o 2 | |
| 2127 Generate the consensus sequence for one diploid individual: | |
| 2128 .EX 2 | |
| 2129 samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fq | |
| 2130 .EE | |
| 2131 .IP o 2 | |
| 2132 Phase one individual: | |
| 2133 .EX 2 | |
| 2134 samtools calmd -AEur aln.bam ref.fa | samtools phase -b prefix - > phase.out | |
| 2135 .EE | |
| 2136 The | |
| 2137 .B calmd | |
| 2138 command is used to reduce false heterozygotes around INDELs. | |
| 2139 | |
| 2140 | |
| 2141 .IP o 2 | |
| 2142 Dump BAQ applied alignment for other SNP callers: | |
| 2143 .EX 2 | |
| 2144 samtools calmd -bAr aln.bam > aln.baq.bam | |
| 2145 .EE | |
| 2146 It adds and corrects the | |
| 2147 .B NM | |
| 2148 and | |
| 2149 .B MD | |
| 2150 tags at the same time. The | |
| 2151 .B calmd | |
| 2152 command also comes with the | |
| 2153 .B -C | |
| 2154 option, the same as the one in | |
| 2155 .B pileup | |
| 2156 and | |
| 2157 .BR mpileup . | |
| 2158 Apply if it helps. | |
| 2159 | |
| 2160 .SH LIMITATIONS | |
| 2161 .PP | |
| 2162 .IP o 2 | |
| 2163 Unaligned words used in bam_import.c, bam_endian.h, bam.c and bam_aux.c. | |
| 2164 .IP o 2 | |
| 2165 Samtools paired-end rmdup does not work for unpaired reads (e.g. orphan | |
| 2166 reads or ends mapped to different chromosomes). If this is a concern, | |
| 2167 please use Picard's MarkDuplicates which correctly handles these cases, | |
| 2168 although a little slower. | |
| 2169 | |
| 2170 .SH AUTHOR | |
| 2171 .PP | |
| 2172 Heng Li from the Sanger Institute wrote the original C version of samtools. | |
| 2173 Bob Handsaker from the Broad Institute implemented the BGZF library. | |
| 2174 James Bonfield from the Sanger Institute developed the CRAM implementation. | |
| 2175 John Marshall and Petr Danecek contribute to the source code and various | |
| 2176 people from the 1000 Genomes Project have contributed to the SAM format | |
| 2177 specification. | |
| 2178 | |
| 2179 .SH SEE ALSO | |
| 2180 .IR bcftools (1), | |
| 2181 .IR sam (5), | |
| 2182 .IR tabix (1) | |
| 2183 .PP | |
| 2184 Samtools website: <http://www.htslib.org/> | |
| 2185 .br | |
| 2186 File format specification of SAM/BAM,CRAM,VCF/BCF: <http://samtools.github.io/hts-specs> | |
| 2187 .br | |
| 2188 Samtools latest source: <https://github.com/samtools/samtools> | |
| 2189 .br | |
| 2190 HTSlib latest source: <https://github.com/samtools/htslib> | |
| 2191 .br | |
| 2192 Bcftools website: <http://samtools.github.io/bcftools> |