jpayne@0: ## htsjdk.samtools.metrics.StringHeader jpayne@0: # MarkDuplicates INPUT=[samples/sample3/reads.sorted.bam] OUTPUT=samples/sample3/reads.sorted.deduped.bam METRICS_FILE=samples/sample3/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 692 9097 0 0 114 2 0 0.006248 20685819 jpayne@0: jpayne@0: ## HISTOGRAM java.lang.Double jpayne@0: BIN VALUE jpayne@0: 1.0 1 jpayne@0: 2.0 1.99956 jpayne@0: 3.0 2.998681 jpayne@0: 4.0 3.997363 jpayne@0: 5.0 4.995605 jpayne@0: 6.0 5.993409 jpayne@0: 7.0 6.990774 jpayne@0: 8.0 7.9877 jpayne@0: 9.0 8.984188 jpayne@0: 10.0 9.980238 jpayne@0: 11.0 10.97585 jpayne@0: 12.0 11.971024 jpayne@0: 13.0 12.965761 jpayne@0: 14.0 13.96006 jpayne@0: 15.0 14.953922 jpayne@0: 16.0 15.947347 jpayne@0: 17.0 16.940336 jpayne@0: 18.0 17.932887 jpayne@0: 19.0 18.925003 jpayne@0: 20.0 19.916682 jpayne@0: 21.0 20.907925 jpayne@0: 22.0 21.898733 jpayne@0: 23.0 22.889104 jpayne@0: 24.0 23.879041 jpayne@0: 25.0 24.868542 jpayne@0: 26.0 25.857608 jpayne@0: 27.0 26.846239 jpayne@0: 28.0 27.834435 jpayne@0: 29.0 28.822197 jpayne@0: 30.0 29.809525 jpayne@0: 31.0 30.796418 jpayne@0: 32.0 31.782878 jpayne@0: 33.0 32.768904 jpayne@0: 34.0 33.754496 jpayne@0: 35.0 34.739655 jpayne@0: 36.0 35.724381 jpayne@0: 37.0 36.708674 jpayne@0: 38.0 37.692534 jpayne@0: 39.0 38.675962 jpayne@0: 40.0 39.658957 jpayne@0: 41.0 40.64152 jpayne@0: 42.0 41.623651 jpayne@0: 43.0 42.60535 jpayne@0: 44.0 43.586618 jpayne@0: 45.0 44.567454 jpayne@0: 46.0 45.547859 jpayne@0: 47.0 46.527833 jpayne@0: 48.0 47.507376 jpayne@0: 49.0 48.486488 jpayne@0: 50.0 49.46517 jpayne@0: 51.0 50.443421 jpayne@0: 52.0 51.421243 jpayne@0: 53.0 52.398634 jpayne@0: 54.0 53.375596 jpayne@0: 55.0 54.352128 jpayne@0: 56.0 55.328231 jpayne@0: 57.0 56.303904 jpayne@0: 58.0 57.279149 jpayne@0: 59.0 58.253965 jpayne@0: 60.0 59.228352 jpayne@0: 61.0 60.202311 jpayne@0: 62.0 61.175842 jpayne@0: 63.0 62.148945 jpayne@0: 64.0 63.121619 jpayne@0: 65.0 64.093866 jpayne@0: 66.0 65.065686 jpayne@0: 67.0 66.037078 jpayne@0: 68.0 67.008044 jpayne@0: 69.0 67.978582 jpayne@0: 70.0 68.948694 jpayne@0: 71.0 69.918379 jpayne@0: 72.0 70.887638 jpayne@0: 73.0 71.85647 jpayne@0: 74.0 72.824877 jpayne@0: 75.0 73.792858 jpayne@0: 76.0 74.760413 jpayne@0: 77.0 75.727543 jpayne@0: 78.0 76.694247 jpayne@0: 79.0 77.660527 jpayne@0: 80.0 78.626382 jpayne@0: 81.0 79.591812 jpayne@0: 82.0 80.556817 jpayne@0: 83.0 81.521399 jpayne@0: 84.0 82.485556 jpayne@0: 85.0 83.449289 jpayne@0: 86.0 84.412599 jpayne@0: 87.0 85.375485 jpayne@0: 88.0 86.337948 jpayne@0: 89.0 87.299987 jpayne@0: 90.0 88.261604 jpayne@0: 91.0 89.222797 jpayne@0: 92.0 90.183569 jpayne@0: 93.0 91.143917 jpayne@0: 94.0 92.103844 jpayne@0: 95.0 93.063348 jpayne@0: 96.0 94.022431 jpayne@0: 97.0 94.981092 jpayne@0: 98.0 95.939331 jpayne@0: 99.0 96.897149 jpayne@0: 100.0 97.854546 jpayne@0: