jpayne@0: ## htsjdk.samtools.metrics.StringHeader jpayne@0: # MarkDuplicates INPUT=[samples/sample1/reads.sorted.bam] OUTPUT=samples/sample1/reads.sorted.deduped.bam METRICS_FILE=samples/sample1/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 20:46:11 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 647 9131 0 0 106 2 0 0.005817 20840746 jpayne@0: jpayne@0: ## HISTOGRAM java.lang.Double jpayne@0: BIN VALUE jpayne@0: 1.0 1 jpayne@0: 2.0 1.999562 jpayne@0: 3.0 2.998686 jpayne@0: 4.0 3.997373 jpayne@0: 5.0 4.995622 jpayne@0: 6.0 5.993433 jpayne@0: 7.0 6.990808 jpayne@0: 8.0 7.987746 jpayne@0: 9.0 8.984247 jpayne@0: 10.0 9.980311 jpayne@0: 11.0 10.97594 jpayne@0: 12.0 11.971132 jpayne@0: 13.0 12.965888 jpayne@0: 14.0 13.960208 jpayne@0: 15.0 14.954093 jpayne@0: 16.0 15.947543 jpayne@0: 17.0 16.940557 jpayne@0: 18.0 17.933137 jpayne@0: 19.0 18.925281 jpayne@0: 20.0 19.916991 jpayne@0: 21.0 20.908267 jpayne@0: 22.0 21.899109 jpayne@0: 23.0 22.889516 jpayne@0: 24.0 23.879489 jpayne@0: 25.0 24.869029 jpayne@0: 26.0 25.858136 jpayne@0: 27.0 26.846809 jpayne@0: 28.0 27.835049 jpayne@0: 29.0 28.822856 jpayne@0: 30.0 29.810231 jpayne@0: 31.0 30.797173 jpayne@0: 32.0 31.783683 jpayne@0: 33.0 32.76976 jpayne@0: 34.0 33.755406 jpayne@0: 35.0 34.74062 jpayne@0: 36.0 35.725402 jpayne@0: 37.0 36.709753 jpayne@0: 38.0 37.693673 jpayne@0: 39.0 38.677162 jpayne@0: 40.0 39.66022 jpayne@0: 41.0 40.642847 jpayne@0: 42.0 41.625044 jpayne@0: 43.0 42.606811 jpayne@0: 44.0 43.588148 jpayne@0: 45.0 44.569054 jpayne@0: 46.0 45.549532 jpayne@0: 47.0 46.529579 jpayne@0: 48.0 47.509198 jpayne@0: 49.0 48.488387 jpayne@0: 50.0 49.467147 jpayne@0: 51.0 50.445479 jpayne@0: 52.0 51.423382 jpayne@0: 53.0 52.400857 jpayne@0: 54.0 53.377903 jpayne@0: 55.0 54.354522 jpayne@0: 56.0 55.330712 jpayne@0: 57.0 56.306476 jpayne@0: 58.0 57.281811 jpayne@0: 59.0 58.25672 jpayne@0: 60.0 59.231201 jpayne@0: 61.0 60.205256 jpayne@0: 62.0 61.178884 jpayne@0: 63.0 62.152085 jpayne@0: 64.0 63.12486 jpayne@0: 65.0 64.097209 jpayne@0: 66.0 65.069132 jpayne@0: 67.0 66.04063 jpayne@0: 68.0 67.011702 jpayne@0: 69.0 67.982348 jpayne@0: 70.0 68.952569 jpayne@0: 71.0 69.922366 jpayne@0: 72.0 70.891737 jpayne@0: 73.0 71.860684 jpayne@0: 74.0 72.829206 jpayne@0: 75.0 73.797305 jpayne@0: 76.0 74.764979 jpayne@0: 77.0 75.732229 jpayne@0: 78.0 76.699055 jpayne@0: 79.0 77.665459 jpayne@0: 80.0 78.631438 jpayne@0: 81.0 79.596995 jpayne@0: 82.0 80.562128 jpayne@0: 83.0 81.526839 jpayne@0: 84.0 82.491128 jpayne@0: 85.0 83.454994 jpayne@0: 86.0 84.418437 jpayne@0: 87.0 85.381459 jpayne@0: 88.0 86.344059 jpayne@0: 89.0 87.306237 jpayne@0: 90.0 88.267994 jpayne@0: 91.0 89.229329 jpayne@0: 92.0 90.190243 jpayne@0: 93.0 91.150737 jpayne@0: 94.0 92.11081 jpayne@0: 95.0 93.070462 jpayne@0: 96.0 94.029693 jpayne@0: 97.0 94.988505 jpayne@0: 98.0 95.946897 jpayne@0: 99.0 96.904868 jpayne@0: 100.0 97.862421 jpayne@0: