| Previous changeset 50:e90a783a4e8b (2019-05-09) Next changeset 52:0acc1975bbeb (2020-11-05) |
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Commit message:
planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty |
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modified:
6_merge_vcfs.xml |
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removed:
test-data/samples/sample1/consensus_preserved.fasta test-data/samples/sample1/reads.all.pileup test-data/samples/sample1/var.flt_preserved.vcf test-data/snplist.txt |
| 6_merge_vcfs.xml |
| diff -r e90a783a4e8b -r 568eb62c7524 6_merge_vcfs.xml |
| 6_merge_vcfs.xml |
| --- a/6_merge_vcfs.xml Thu May 09 11:45:22 2019 -0400 +++ b/6_merge_vcfs.xml Tue Sep 17 11:06:59 2019 -0400 @@ -10,8 +10,6 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && - ls -lah \$CONDA_DEFAULT_ENV/bin && - ls -lah \$CONDA_DEFAULT_ENV/lib && python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" #for $vcf in $vcfs -n $vcf.element_identifier -f $vcf |
| test-data/samples/sample1/consensus_preserved.fasta |
| diff -r e90a783a4e8b -r 568eb62c7524 test-data/samples/sample1/consensus_preserved.fasta |
| test-data/samples/sample1/consensus_preserved.fasta |
| --- a/test-data/samples/sample1/consensus_preserved.fasta Thu May 09 11:45:22 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->sample1 -GCACGGCGCGATCCGAATTGCAGGGCGTACCTGGACCCCGGTGACGGGGGATCGGGGACT -CTTGGTGAGGAACTAAAACGACGTTTTCATGGCGACTGCTTGGTGTCAGCACATTCCCTA -TATCGGTGGACACGTA |
| test-data/samples/sample1/reads.all.pileup |
| diff -r e90a783a4e8b -r 568eb62c7524 test-data/samples/sample1/reads.all.pileup |
| test-data/samples/sample1/reads.all.pileup |
| --- a/test-data/samples/sample1/reads.all.pileup Thu May 09 11:45:22 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48502 +0,0 @@ -gi|9626243|ref|NC_001416.1| 1 G 0 * * -gi|9626243|ref|NC_001416.1| 2 G 0 * * -gi|9626243|ref|NC_001416.1| 3 G 0 * * -gi|9626243|ref|NC_001416.1| 4 C 1 . < -gi|9626243|ref|NC_001416.1| 5 G 5 ..... 0.17/ -gi|9626243|ref|NC_001416.1| 6 G 5 ...A. 2032C -gi|9626243|ref|NC_001416.1| 7 C 3 ... /2F -gi|9626243|ref|NC_001416.1| 8 G 5 ..N.. /:E.. -gi|9626243|ref|NC_001416.1| 9 A 4 .... 5341 -gi|9626243|ref|NC_001416.1| 10 C 4 ...N 8=/6 -gi|9626243|ref|NC_001416.1| 11 C 3 ... 0>D -gi|9626243|ref|NC_001416.1| 12 T 4 .... 5EF6 -gi|9626243|ref|NC_001416.1| 13 C 4 .... G<<H -gi|9626243|ref|NC_001416.1| 14 G 7 ....... .;60=7A -gi|9626243|ref|NC_001416.1| 15 C 4 .... ?20F -gi|9626243|ref|NC_001416.1| 16 G 6 ...... ?H=?.= -gi|9626243|ref|NC_001416.1| 17 G 5 ..... ?D24; -gi|9626243|ref|NC_001416.1| 18 G 5 ..... BEDC; -gi|9626243|ref|NC_001416.1| 19 T 7 .N..... <E23@:= -gi|9626243|ref|NC_001416.1| 20 T 4 .... 6>B7 -gi|9626243|ref|NC_001416.1| 21 T 4 .... ;D4@ -gi|9626243|ref|NC_001416.1| 22 T 5 ..... :<528 -gi|9626243|ref|NC_001416.1| 23 C 2 .. 0= -gi|9626243|ref|NC_001416.1| 24 G 3 ... ;;: -gi|9626243|ref|NC_001416.1| 25 C 7 ....... 81<=0@6 -gi|9626243|ref|NC_001416.1| 26 T 7 ....... F.AB0/8 -gi|9626243|ref|NC_001416.1| 27 A 7 ....N.. 3@<5C;9 -gi|9626243|ref|NC_001416.1| 28 T 6 ...C.. 4A1/H? -gi|9626243|ref|NC_001416.1| 29 T 5 ..... 69?3< -gi|9626243|ref|NC_001416.1| 30 T 4 .... <FH; -gi|9626243|ref|NC_001416.1| 31 A 5 ..... :B?;< -gi|9626243|ref|NC_001416.1| 32 T 6 ..N... /A?0A4 -gi|9626243|ref|NC_001416.1| 33 G 7 ....... 705FG01 -gi|9626243|ref|NC_001416.1| 34 A 5 ..... C>8F> -gi|9626243|ref|NC_001416.1| 35 A 6 ...... E@;9DG -gi|9626243|ref|NC_001416.1| 36 A 6 .C.... :C/;4G -gi|9626243|ref|NC_001416.1| 37 A 5 ..... ;1:A0 -gi|9626243|ref|NC_001416.1| 38 T 7 ....... /7>H63; -gi|9626243|ref|NC_001416.1| 39 T 8 ........ /=6F2G8C -gi|9626243|ref|NC_001416.1| 40 T 9 ......... 8=5FH0/;@ -gi|9626243|ref|NC_001416.1| 41 T 6 ...... 69C03. -gi|9626243|ref|NC_001416.1| 42 C 7 ......^K. =:@>39B -gi|9626243|ref|NC_001416.1| 43 C 8 ........ 1;D330/A -gi|9626243|ref|NC_001416.1| 44 G 5 ..... >0>7? -gi|9626243|ref|NC_001416.1| 45 G 7 ...$.... A=49>96 -gi|9626243|ref|NC_001416.1| 46 T 9 ......... 5>>H:>56; -gi|9626243|ref|NC_001416.1| 47 T 6 ...... 6>1H<H -gi|9626243|ref|NC_001416.1| 48 T 6 ..N... G8E93F -gi|9626243|ref|NC_001416.1| 49 A 5 ..... HF<F> -gi|9626243|ref|NC_001416.1| 50 A 8 ........ C3C75:A9 -gi|9626243|ref|NC_001416.1| 51 G 4 .... EABC -gi|9626243|ref|NC_001416.1| 52 G 7 ....$... A69>0.1 -gi|9626243|ref|NC_001416.1| 53 C 6 ...... 1EHDGB -gi|9626243|ref|NC_001416.1| 54 G 6 ...... A:90/8 -gi|9626243|ref|NC_001416.1| 55 T 8 ........ =56B81CD -gi|9626243|ref|NC_001416.1| 56 T 7 ....... @B=6G7H -gi|9626243|ref|NC_001416.1| 57 T 6 ...... 5:GA=F -gi|9626243|ref|NC_001416.1| 58 C 6 ...... .H?@5B -gi|9626243|ref|NC_001416.1| 59 C 7 ....... /F7AB/D -gi|9626243|ref|NC_001416.1| 60 G 4 .... H<7H -gi|9626243|ref|NC_001416.1| 61 T 9 ......... C/2640>9E -gi|9626243|ref|NC_001416.1| 62 T 6 ...... @0>9;0 -gi|9626243|ref|NC_001416.1| 63 C 6 ...... 4@?DB2 -gi|9626243|ref|NC_001416.1| 64 T 7 ......^K. =5/2H70 -gi|9626243|ref|NC_001416.1| 65 T 8 ........ @:8<47G? -gi|9626243|ref|NC_001416.1| 66 C 6 ...... 7=:G=E -gi|9626243|ref|NC_001416.1| 67 T 4 .... 7201 -gi|9626243|ref|NC_001416.1| 68 T 6 ...... >G=3<D -gi|9626243|ref|NC_001416.1| 69 C 9 ......... 1<H@.>=>2 -gi|9626243|ref|NC_001416.1| 70 G 5 ..... EC810 -gi|9626243|ref|NC_001416.1| 71 T 7 ....... G41?E?G -gi|9626243|ref|NC_001416.1| 72 C 8 .N...... 8F6409.@ -gi|9626243|ref|NC_001416.1| 73 A 8 ....N... >E1AGCCC -gi|9626243|ref|NC_001416.1| 74 T 8 N......^K. E./1?D27 -gi|9626243|ref|NC_001416.1| 75 A 10 .......... 37;>:?1?0? -gi|9626243|ref|NC_001416.1| 76 A 9 ......... D99.46479 -gi|9626243|ref|NC_001416.1| 77 C 9 ......... H3@H2:0@A -gi|9626243|ref|NC_001416.1| 78 T 8 ..E0C@ -gi|9626243|ref|NC_001416.1| 48427 C 7 ,,,,,,, A@;H@2= -gi|9626243|ref|NC_001416.1| 48428 T 8 ,,,,,,,, 9<4CE/?B -gi|9626243|ref|NC_001416.1| 48429 C 11 ,,,,,,,,,,, <GBFHD2DH;/ -gi|9626243|ref|NC_001416.1| 48430 C 10 ,,,,,,,,,, 21AB79BE<: -gi|9626243|ref|NC_001416.1| 48431 A 9 ,,,,,,,,, GF.A2;12: -gi|9626243|ref|NC_001416.1| 48432 C 6 ,,,,,, H@?E7B -gi|9626243|ref|NC_001416.1| 48433 G 7 ,,,,,,, >;D4B@D -gi|9626243|ref|NC_001416.1| 48434 C 7 ,n,,,,, ./:01;> -gi|9626243|ref|NC_001416.1| 48435 A 8 ,,,,,,,, 2<617910 -gi|9626243|ref|NC_001416.1| 48436 C 8 ,,,,,,,, @455A4@; -gi|9626243|ref|NC_001416.1| 48437 G 9 ,,,,,,,,, C;>D/>4G1 -gi|9626243|ref|NC_001416.1| 48438 T 6 ,,,,,^K, >/F8<B -gi|9626243|ref|NC_001416.1| 48439 T 8 ,,,,,,,, 21.?/F<0 -gi|9626243|ref|NC_001416.1| 48440 G 8 ,,,,,,,, :6<8;7>1 -gi|9626243|ref|NC_001416.1| 48441 T 4 ,,,, 5;7. -gi|9626243|ref|NC_001416.1| 48442 G 10 n,,,,,,,,, 4D84>.G5H2 -gi|9626243|ref|NC_001416.1| 48443 A 8 ,,,,,,,, 5==92E/2 -gi|9626243|ref|NC_001416.1| 48444 T 9 ,n,,,,,,, =@C2;0CFE -gi|9626243|ref|NC_001416.1| 48445 A 8 ,,,,n,,^K, G=2<D>>; -gi|9626243|ref|NC_001416.1| 48446 T 7 ,,,,,,, 3H=F7=2 -gi|9626243|ref|NC_001416.1| 48447 G 10 ,,,,,,,,,, 16@C3@:0C1 -gi|9626243|ref|NC_001416.1| 48448 T 10 ,,,,,,,,,, C=?45E75AD -gi|9626243|ref|NC_001416.1| 48449 A 8 ,,,,,,,, G.@C47DD -gi|9626243|ref|NC_001416.1| 48450 G 9 ,,,,,,,,, A<.>C23A7 -gi|9626243|ref|NC_001416.1| 48451 A 6 ,,,,,$, 0.5>A; -gi|9626243|ref|NC_001416.1| 48452 T 8 ,,,,,,,, 86B<7H/9 -gi|9626243|ref|NC_001416.1| 48453 G 6 ,,,,,, ?;299: -gi|9626243|ref|NC_001416.1| 48454 A 6 ,$n,,,, 0@G.@? -gi|9626243|ref|NC_001416.1| 48455 T 5 ,,,,, 2<G;6 -gi|9626243|ref|NC_001416.1| 48456 A 6 ,,,,,, @48.=4 -gi|9626243|ref|NC_001416.1| 48457 A 6 ,,,,,, =E:9HH -gi|9626243|ref|NC_001416.1| 48458 T 5 ,,,,, ><2D4 -gi|9626243|ref|NC_001416.1| 48459 C 3 ,,, 5<G -gi|9626243|ref|NC_001416.1| 48460 A 7 ,,,,,,, 001:C5> -gi|9626243|ref|NC_001416.1| 48461 T 4 ,,,, 2496 -gi|9626243|ref|NC_001416.1| 48462 T 5 ,,,,, 0C31H -gi|9626243|ref|NC_001416.1| 48463 A 5 ,,,,, /30B7 -gi|9626243|ref|NC_001416.1| 48464 T 7 ,,,,,,, A4G<@07 -gi|9626243|ref|NC_001416.1| 48465 C 8 ,,,,,,,, D<AE.;1C -gi|9626243|ref|NC_001416.1| 48466 A 5 ,,,,, 5C;C7 -gi|9626243|ref|NC_001416.1| 48467 C 5 ,,n,, E@6F0 -gi|9626243|ref|NC_001416.1| 48468 T 7 ,,,,,,, ;42:772 -gi|9626243|ref|NC_001416.1| 48469 T 6 ,,,,,, :66F@H -gi|9626243|ref|NC_001416.1| 48470 T 6 ,$,,,,, =4/H4B -gi|9626243|ref|NC_001416.1| 48471 A 7 ,,,,,,, 81/601/ -gi|9626243|ref|NC_001416.1| 48472 C 7 ,,,,,,, D<F2:HD -gi|9626243|ref|NC_001416.1| 48473 G 5 ,,,,, HFH5E -gi|9626243|ref|NC_001416.1| 48474 G 5 ,,,$,, ;>315 -gi|9626243|ref|NC_001416.1| 48475 G 5 ,,,,$, 8.:4> -gi|9626243|ref|NC_001416.1| 48476 T 3 ,,, 375 -gi|9626243|ref|NC_001416.1| 48477 C 5 ,,,,, >C839 -gi|9626243|ref|NC_001416.1| 48478 C 5 ,,,,, 6:0>. -gi|9626243|ref|NC_001416.1| 48479 T 5 ,,,,, E83.F -gi|9626243|ref|NC_001416.1| 48480 T 4 aaaa ?3./ -gi|9626243|ref|NC_001416.1| 48481 T 4 ,,,, 91A7 -gi|9626243|ref|NC_001416.1| 48482 C 4 ,,,, 1;@0 -gi|9626243|ref|NC_001416.1| 48483 C 3 n,, 21@ -gi|9626243|ref|NC_001416.1| 48484 G 4 ,$,,, :CC; -gi|9626243|ref|NC_001416.1| 48485 G 5 ,,,,, D@F48 -gi|9626243|ref|NC_001416.1| 48486 T 4 ,,$,, 5/5. -gi|9626243|ref|NC_001416.1| 48487 G 3 ,,, >C@ -gi|9626243|ref|NC_001416.1| 48488 A 4 ,,,, 5=>= -gi|9626243|ref|NC_001416.1| 48489 T 4 ,,,,$ C97C -gi|9626243|ref|NC_001416.1| 48490 C 0 * * -gi|9626243|ref|NC_001416.1| 48491 C 2 ,, 3F -gi|9626243|ref|NC_001416.1| 48492 G 2 ,, G. -gi|9626243|ref|NC_001416.1| 48493 A 3 ,,, 3.: -gi|9626243|ref|NC_001416.1| 48494 C 3 ,,, ?H< -gi|9626243|ref|NC_001416.1| 48495 A 3 ,,, 7HE -gi|9626243|ref|NC_001416.1| 48496 G 2 ,, 1> -gi|9626243|ref|NC_001416.1| 48497 G 2 ,+14ttaccggtgattct,+1t 5? -gi|9626243|ref|NC_001416.1| 48498 T 0 * * -gi|9626243|ref|NC_001416.1| 48499 T 0 * * -gi|9626243|ref|NC_001416.1| 48500 A 0 * * -gi|9626243|ref|NC_001416.1| 48501 C 0 * * -gi|9626243|ref|NC_001416.1| 48502 G 1 ,$ 4 |
| test-data/samples/sample1/var.flt_preserved.vcf |
| diff -r e90a783a4e8b -r 568eb62c7524 test-data/samples/sample1/var.flt_preserved.vcf |
| test-data/samples/sample1/var.flt_preserved.vcf |
| --- a/test-data/samples/sample1/var.flt_preserved.vcf Thu May 09 11:45:22 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -##fileformat=VCFv4.1 -##source=VarScan2 -##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15"> -##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)"> -##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant"> -##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant"> -##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15"> -##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> -##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> -##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> -##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test"> -##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)"> -##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)"> -##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> -##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> -##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> -##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> -##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> -##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 -gi|9626243|ref|NC_001416.1| 753 . G A . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:25:24:0:23:100%:1.2146E-13:0:27:0:0:15:8 -gi|9626243|ref|NC_001416.1| 3351 . C G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:24:22:0:22:100%:4.7526E-13:0:28:0:0:10:12 -gi|9626243|ref|NC_001416.1| 3656 . T G . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:25:23:0:23:100%:1.2146E-13:0:25:0:0:12:11 -gi|9626243|ref|NC_001416.1| 6824 . A C . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:10:8 -gi|9626243|ref|NC_001416.1| 7897 . G A . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:26:23:0:23:100%:1.2146E-13:0:25:0:0:11:12 -gi|9626243|ref|NC_001416.1| 9175 . A G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:22:22:0:22:100%:4.7526E-13:0:28:0:0:8:14 -gi|9626243|ref|NC_001416.1| 12717 . G C . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:29:25:0:24:100%:3.101E-14:0:28:0:0:10:14 -gi|9626243|ref|NC_001416.1| 12795 . C T . PASS ADP=26;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:146:27:26:0:26:100%:2.0165E-15:0:29:0:0:16:10 -gi|9626243|ref|NC_001416.1| 12959 . T G . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:22:21:0:21:100%:1.8578E-12:0:25:0:0:13:8 -gi|9626243|ref|NC_001416.1| 16654 . C G . PASS ADP=23;WT=0;HET=0..Q:ABQ:RDF:RDR:ADF:ADR 1/1:129:24:23:0:23:100%:1.2146E-13:0:26:0:0:14:9 -gi|9626243|ref|NC_001416.1| 16715 . T G . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:19:18:0:18:100%:1.1019E-10:0:25:0:0:8:10 -gi|9626243|ref|NC_001416.1| 18598 . C G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:25:22:0:22:100%:4.7526E-13:0:24:0:0:12:10 -gi|9626243|ref|NC_001416.1| 19469 . G T . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:21:18:0:18:100%:1.1019E-10:0:28:0:0:11:7 -gi|9626243|ref|NC_001416.1| 20099 . C T . PASS ADP=28;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:158:28:28:0:28:100%:1.3074E-16:0:29:0:0:14:14 -gi|9626243|ref|NC_001416.1| 21110 . T G . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:18:16:0:16:100%:1.6637E-9:0:26:0:0:5:11 -gi|9626243|ref|NC_001416.1| 23362 . T A . PASS ADP=11;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:58:14:11:0:11:100%:1.4176E-6:0:26:0:0:3:8 -gi|9626243|ref|NC_001416.1| 24319 . G T . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:7:11 -gi|9626243|ref|NC_001416.1| 24766 . G A . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:19:17:0:17:100%:4.2852E-10:0:24:0:0:6:11 -gi|9626243|ref|NC_001416.1| 29891 . G C . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:21:20:0:20:100%:7.2544E-12:0:26:0:0:9:11 -gi|9626243|ref|NC_001416.1| 31551 . A G . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:16:15:0:15:100%:6.4467E-9:0:25:0:0:7:8 -gi|9626243|ref|NC_001416.1| 32086 . T A . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:69:17:15:1:14:93.33%:1.0315E-7:33:28:1:0:7:7 -gi|9626243|ref|NC_001416.1| 33000 . C T . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:18:17:0:17:100%:4.2852E-10:0:26:0:0:7:10 -gi|9626243|ref|NC_001416.1| 33591 . T G . PASS ADP=30;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:170:30:30:0:30:100%:8.4556E-18:0:26:0:0:16:14 -gi|9626243|ref|NC_001416.1| 36010 . C T . PASS ADP=9;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:46:9:9:0:9:100%:2.0568E-5:0:26:0:0:0:9 -gi|9626243|ref|NC_001416.1| 37208 . G C . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:19:19:0:19:100%:2.8292E-11:0:29:0:0:8:11 -gi|9626243|ref|NC_001416.1| 38165 . T C . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:152:29:27:0:27:100%:5.1363E-16:0:23:0:0:17:10 -gi|9626243|ref|NC_001416.1| 39485 . A C . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:20:20:0:20:100%:7.2544E-12:0:29:0:0:10:10 -gi|9626243|ref|NC_001416.1| 40457 . T C . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:138:28:27:1:26:96.3%:1.4382E-14:24:25:1:0:11:15 -gi|9626243|ref|NC_001416.1| 42439 . A C . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:28:24:0:24:100%:3.101E-14:0:26:0:0:16:8 -gi|9626243|ref|NC_001416.1| 43306 . T G . PASS ADP=32;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:176:33:32:0:31:100%:2.1486E-18:0:27:0:0:11:20 -gi|9626243|ref|NC_001416.1| 46237 . G A . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:152:27:27:0:27:100%:5.1363E-16:0:26:0:0:12:15 -gi|9626243|ref|NC_001416.1| 47893 . G A . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:28:23:0:23:100%:1.2146E-13:0:25:0:0:12:11 |
| test-data/snplist.txt |
| diff -r e90a783a4e8b -r 568eb62c7524 test-data/snplist.txt |
| test-data/snplist.txt |
| --- a/test-data/snplist.txt Thu May 09 11:45:22 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,165 +0,0 @@ -gi|9626243|ref|NC_001416.1| 403 1 sample1 -gi|9626243|ref|NC_001416.1| 550 1 sample4 -gi|9626243|ref|NC_001416.1| 586 1 sample4 -gi|9626243|ref|NC_001416.1| 753 1 sample1 -gi|9626243|ref|NC_001416.1| 1019 1 sample4 -gi|9626243|ref|NC_001416.1| 1079 1 sample1 -gi|9626243|ref|NC_001416.1| 1540 1 sample1 -gi|9626243|ref|NC_001416.1| 1620 1 sample4 -gi|9626243|ref|NC_001416.1| 1650 1 sample4 -gi|9626243|ref|NC_001416.1| 1788 1 sample4 -gi|9626243|ref|NC_001416.1| 1804 1 sample1 -gi|9626243|ref|NC_001416.1| 2123 1 sample1 -gi|9626243|ref|NC_001416.1| 2439 1 sample3 -gi|9626243|ref|NC_001416.1| 2452 1 sample4 -gi|9626243|ref|NC_001416.1| 2599 1 sample2 -gi|9626243|ref|NC_001416.1| 3063 1 sample4 -gi|9626243|ref|NC_001416.1| 3351 1 sample1 -gi|9626243|ref|NC_001416.1| 3648 1 sample3 -gi|9626243|ref|NC_001416.1| 3656 1 sample1 -gi|9626243|ref|NC_001416.1| 3678 1 sample2 -gi|9626243|ref|NC_001416.1| 4977 1 sample1 -gi|9626243|ref|NC_001416.1| 5142 1 sample2 -gi|9626243|ref|NC_001416.1| 5336 1 sample2 -gi|9626243|ref|NC_001416.1| 5462 1 sample3 -gi|9626243|ref|NC_001416.1| 5482 1 sample1 -gi|9626243|ref|NC_001416.1| 5516 1 sample1 -gi|9626243|ref|NC_001416.1| 5800 1 sample1 -gi|9626243|ref|NC_001416.1| 5818 1 sample4 -gi|9626243|ref|NC_001416.1| 5994 1 sample2 -gi|9626243|ref|NC_001416.1| 6296 1 sample4 -gi|9626243|ref|NC_001416.1| 6535 1 sample2 -gi|9626243|ref|NC_001416.1| 6824 1 sample1 -gi|9626243|ref|NC_001416.1| 7424 1 sample2 -gi|9626243|ref|NC_001416.1| 7668 1 sample3 -gi|9626243|ref|NC_001416.1| 7897 1 sample1 -gi|9626243|ref|NC_001416.1| 8420 1 sample3 -gi|9626243|ref|NC_001416.1| 8938 1 sample4 -gi|9626243|ref|NC_001416.1| 9175 1 sample1 -gi|9626243|ref|NC_001416.1| 9234 1 sample4 -gi|9626243|ref|NC_001416.1| 9919 1 sample3 -gi|9626243|ref|NC_001416.1| 10127 1 sample2 -gi|9626243|ref|NC_001416.1| 10264 1 sample3 -gi|9626243|ref|NC_001416.1| 10421 1 sample4 -gi|9626243|ref|NC_001416.1| 10568 1 sample4 -gi|9626243|ref|NC_001416.1| 11066 1 sample3 -gi|9626243|ref|NC_001416.1| 11128 1 sample4 -gi|9626243|ref|NC_001416.1| 11782 1 sample2 -gi|9626243|ref|NC_001416.1| 12070 1 sample3 -gi|9626243|ref|NC_001416.1| 12717 1 sample1 -gi|9626243|ref|NC_001416.1| 12795 1 sample1 -gi|9626243|ref|NC_001416.1| 12876 1 sample4 -gi|9626243|ref|NC_001416.1| 12959 1 sample1 -gi|9626243|ref|NC_001416.1| 12970 1 sample3 -gi|9626243|ref|NC_001416.1| 13107 1 sample3 -gi|9626243|ref|NC_001416.1| 13264 1 sample2 -gi|9626243|ref|NC_001416.1| 13542 1 sample2 -gi|9626243|ref|NC_001416.1| 13647 1 sample4 -gi|9626243|ref|NC_001416.1| 13952 1 sample2 -gi|9626243|ref|NC_001416.1| 13971 1 sample3 -gi|9626243|ref|NC_001416.1| 15384 1 sample3 -gi|9626243|ref|NC_001416.1| 15715 1 sample2 -gi|9626243|ref|NC_001416.1| 15967 1 sample2 -gi|9626243|ref|NC_001416.1| 16070 1 sample3 -gi|9626243|ref|NC_001416.1| 16654 1 sample1 -gi|9626243|ref|NC_001416.1| 16715 1 sample1 -gi|9626243|ref|NC_001416.1| 17142 1 sample2 -gi|9626243|ref|NC_001416.1| 17311 1 sample2 -gi|9626243|ref|NC_001416.1| 17854 1 sample2 -gi|9626243|ref|NC_001416.1| 18151 1 sample3 -gi|9626243|ref|NC_001416.1| 18188 1 sample4 -gi|9626243|ref|NC_001416.1| 18210 1 sample4 -gi|9626243|ref|NC_001416.1| 18420 1 sample2 -gi|9626243|ref|NC_001416.1| 18598 1 sample1 -gi|9626243|ref|NC_001416.1| 18652 1 sample2 -gi|9626243|ref|NC_001416.1| 18989 1 sample3 -gi|9626243|ref|NC_001416.1| 19208 1 sample2 -gi|9626243|ref|NC_001416.1| 19448 1 sample3 -gi|9626243|ref|NC_001416.1| 19469 1 sample1 -gi|9626243|ref|NC_001416.1| 20079 1 sample3 -gi|9626243|ref|NC_001416.1| 20099 1 sample1 -gi|9626243|ref|NC_001416.1| 20289 1 sample3 -gi|9626243|ref|NC_001416.1| 20367 1 sample2 -gi|9626243|ref|NC_001416.1| 21110 1 sample1 -gi|9626243|ref|NC_001416.1| 21320 1 sample2 -gi|9626243|ref|NC_001416.1| 21653 1 sample3 -gi|9626243|ref|NC_001416.1| 22220 1 sample2 -gi|9626243|ref|NC_001416.1| 22357 1 sample4 -gi|9626243|ref|NC_001416.1| 22747 1 sample2 -gi|9626243|ref|NC_001416.1| 23362 1 sample1 -gi|9626243|ref|NC_001416.1| 23457 1 sample2 -gi|9626243|ref|NC_001416.1| 24043 1 sample4 -gi|9626243|ref|NC_001416.1| 24319 1 sample1 -gi|9626243|ref|NC_001416.1| 24766 1 sample1 -gi|9626243|ref|NC_001416.1| 24930 1 sample3 -gi|9626243|ref|NC_001416.1| 25005 1 sample2 -gi|9626243|ref|NC_001416.1| 25158 1 sample2 -gi|9626243|ref|NC_001416.1| 25645 1 sample2 -gi|9626243|ref|NC_001416.1| 26173 1 sample2 -gi|9626243|ref|NC_001416.1| 26728 1 sample3 -gi|9626243|ref|NC_001416.1| 26972 1 sample4 -gi|9626243|ref|NC_001416.1| 27412 1 sample3 -gi|9626243|ref|NC_001416.1| 27539 1 sample4 -gi|9626243|ref|NC_001416.1| 27661 1 sample2 -gi|9626243|ref|NC_001416.1| 27722 1 sample4 -gi|9626243|ref|NC_001416.1| 27790 1 sample1 -gi|9626243|ref|NC_001416.1| 27825 1 sample4 -gi|9626243|ref|NC_001416.1| 27834 1 sample3 -gi|9626243|ref|NC_001416.1| 28045 1 sample2 -gi|9626243|ref|NC_001416.1| 28362 1 sample2 -gi|9626243|ref|NC_001416.1| 29265 1 sample4 -gi|9626243|ref|NC_001416.1| 29411 1 sample2 -gi|9626243|ref|NC_001416.1| 29435 1 sample3 -gi|9626243|ref|NC_001416.1| 29891 1 sample1 -gi|9626243|ref|NC_001416.1| 30125 1 sample2 -gi|9626243|ref|NC_001416.1| 30757 1 sample3 -gi|9626243|ref|NC_001416.1| 30890 1 sample3 -gi|9626243|ref|NC_001416.1| 31328 1 sample3 -gi|9626243|ref|NC_001416.1| 31363 1 sample4 -gi|9626243|ref|NC_001416.1| 31551 1 sample1 -gi|9626243|ref|NC_001416.1| 32086 1 sample1 -gi|9626243|ref|NC_001416.1| 32660 1 sample3 -gi|9626243|ref|NC_001416.1| 33000 1 sample1 -gi|9626243|ref|NC_001416.1| 33591 1 sample1 -gi|9626243|ref|NC_001416.1| 33612 1 sample4 -gi|9626243|ref|NC_001416.1| 33865 1 sample3 -gi|9626243|ref|NC_001416.1| 34137 1 sample2 -gi|9626243|ref|NC_001416.1| 34370 1 sample1 -gi|9626243|ref|NC_001416.1| 34812 1 sample1 -gi|9626243|ref|NC_001416.1| 34920 1 sample1 -gi|9626243|ref|NC_001416.1| 35148 1 sample1 -gi|9626243|ref|NC_001416.1| 35802 1 sample3 -gi|9626243|ref|NC_001416.1| 35907 1 sample2 -gi|9626243|ref|NC_001416.1| 36010 1 sample1 -gi|9626243|ref|NC_001416.1| 36169 1 sample3 -gi|9626243|ref|NC_001416.1| 36642 1 sample4 -gi|9626243|ref|NC_001416.1| 37208 1 sample1 -gi|9626243|ref|NC_001416.1| 37387 1 sample4 -gi|9626243|ref|NC_001416.1| 37519 1 sample3 -gi|9626243|ref|NC_001416.1| 37898 1 sample3 -gi|9626243|ref|NC_001416.1| 38073 1 sample3 -gi|9626243|ref|NC_001416.1| 38165 1 sample1 -gi|9626243|ref|NC_001416.1| 38575 1 sample2 -gi|9626243|ref|NC_001416.1| 39003 1 sample3 -gi|9626243|ref|NC_001416.1| 39206 1 sample2 -gi|9626243|ref|NC_001416.1| 39484 1 sample2 -gi|9626243|ref|NC_001416.1| 39485 1 sample1 -gi|9626243|ref|NC_001416.1| 40457 1 sample1 -gi|9626243|ref|NC_001416.1| 40835 1 sample4 -gi|9626243|ref|NC_001416.1| 40984 1 sample4 -gi|9626243|ref|NC_001416.1| 41064 1 sample4 -gi|9626243|ref|NC_001416.1| 41448 1 sample3 -gi|9626243|ref|NC_001416.1| 41954 1 sample4 -gi|9626243|ref|NC_001416.1| 42439 1 sample1 -gi|9626243|ref|NC_001416.1| 43306 1 sample1 -gi|9626243|ref|NC_001416.1| 43470 1 sample2 -gi|9626243|ref|NC_001416.1| 44134 1 sample2 -gi|9626243|ref|NC_001416.1| 44201 1 sample4 -gi|9626243|ref|NC_001416.1| 44413 1 sample2 -gi|9626243|ref|NC_001416.1| 45364 1 sample2 -gi|9626243|ref|NC_001416.1| 45409 1 sample4 -gi|9626243|ref|NC_001416.1| 46237 1 sample1 -gi|9626243|ref|NC_001416.1| 46283 1 sample4 -gi|9626243|ref|NC_001416.1| 46842 1 sample3 -gi|9626243|ref|NC_001416.1| 47425 1 sample2 -gi|9626243|ref|NC_001416.1| 47893 1 sample1 |