jpayne@0: ## htsjdk.samtools.metrics.StringHeader jpayne@0: # MarkDuplicates INPUT=[samples/sample4/reads.sorted.bam] OUTPUT=samples/sample4/reads.sorted.deduped.bam METRICS_FILE=samples/sample4/duplicate_reads_metrics.txt VERBOSITY=WARNING MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false jpayne@0: ## htsjdk.samtools.metrics.StringHeader jpayne@0: # Started on: Wed Jan 03 20:46:32 UTC 2018 jpayne@0: jpayne@0: ## METRICS CLASS picard.sam.DuplicationMetrics jpayne@0: LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE jpayne@0: Unknown Library 655 9117 0 0 103 3 0 0.005771 13850242 jpayne@0: jpayne@0: ## HISTOGRAM java.lang.Double jpayne@0: BIN VALUE jpayne@0: 1.0 1 jpayne@0: 2.0 1.999342 jpayne@0: 3.0 2.998026 jpayne@0: 4.0 3.996053 jpayne@0: 5.0 4.993424 jpayne@0: 6.0 5.990138 jpayne@0: 7.0 6.986196 jpayne@0: 8.0 7.981599 jpayne@0: 9.0 8.976347 jpayne@0: 10.0 9.97044 jpayne@0: 11.0 10.963879 jpayne@0: 12.0 11.956665 jpayne@0: 13.0 12.948797 jpayne@0: 14.0 13.940276 jpayne@0: 15.0 14.931103 jpayne@0: 16.0 15.921277 jpayne@0: 17.0 16.9108 jpayne@0: 18.0 17.899672 jpayne@0: 19.0 18.887894 jpayne@0: 20.0 19.875465 jpayne@0: 21.0 20.862386 jpayne@0: 22.0 21.848658 jpayne@0: 23.0 22.83428 jpayne@0: 24.0 23.819255 jpayne@0: 25.0 24.803581 jpayne@0: 26.0 25.787259 jpayne@0: 27.0 26.77029 jpayne@0: 28.0 27.752674 jpayne@0: 29.0 28.734412 jpayne@0: 30.0 29.715503 jpayne@0: 31.0 30.695949 jpayne@0: 32.0 31.67575 jpayne@0: 33.0 32.654906 jpayne@0: 34.0 33.633418 jpayne@0: 35.0 34.611286 jpayne@0: 36.0 35.58851 jpayne@0: 37.0 36.565092 jpayne@0: 38.0 37.541031 jpayne@0: 39.0 38.516327 jpayne@0: 40.0 39.490982 jpayne@0: 41.0 40.464995 jpayne@0: 42.0 41.438368 jpayne@0: 43.0 42.4111 jpayne@0: 44.0 43.383191 jpayne@0: 45.0 44.354644 jpayne@0: 46.0 45.325457 jpayne@0: 47.0 46.295631 jpayne@0: 48.0 47.265166 jpayne@0: 49.0 48.234064 jpayne@0: 50.0 49.202324 jpayne@0: 51.0 50.169947 jpayne@0: 52.0 51.136933 jpayne@0: 53.0 52.103283 jpayne@0: 54.0 53.068997 jpayne@0: 55.0 54.034076 jpayne@0: 56.0 54.998519 jpayne@0: 57.0 55.962328 jpayne@0: 58.0 56.925503 jpayne@0: 59.0 57.888043 jpayne@0: 60.0 58.849951 jpayne@0: 61.0 59.811225 jpayne@0: 62.0 60.771867 jpayne@0: 63.0 61.731877 jpayne@0: 64.0 62.691255 jpayne@0: 65.0 63.650002 jpayne@0: 66.0 64.608117 jpayne@0: 67.0 65.565603 jpayne@0: 68.0 66.522458 jpayne@0: 69.0 67.478684 jpayne@0: 70.0 68.43428 jpayne@0: 71.0 69.389248 jpayne@0: 72.0 70.343587 jpayne@0: 73.0 71.297298 jpayne@0: 74.0 72.250381 jpayne@0: 75.0 73.202838 jpayne@0: 76.0 74.154668 jpayne@0: 77.0 75.105871 jpayne@0: 78.0 76.056448 jpayne@0: 79.0 77.0064 jpayne@0: 80.0 77.955727 jpayne@0: 81.0 78.904429 jpayne@0: 82.0 79.852507 jpayne@0: 83.0 80.799961 jpayne@0: 84.0 81.746791 jpayne@0: 85.0 82.692999 jpayne@0: 86.0 83.638583 jpayne@0: 87.0 84.583546 jpayne@0: 88.0 85.527887 jpayne@0: 89.0 86.471606 jpayne@0: 90.0 87.414704 jpayne@0: 91.0 88.357182 jpayne@0: 92.0 89.29904 jpayne@0: 93.0 90.240277 jpayne@0: 94.0 91.180896 jpayne@0: 95.0 92.120895 jpayne@0: 96.0 93.060276 jpayne@0: 97.0 93.999039 jpayne@0: 98.0 94.937184 jpayne@0: 99.0 95.874711 jpayne@0: 100.0 96.811622 jpayne@0: