jpayne@0: ## htsjdk.samtools.metrics.StringHeader jpayne@0: # MarkDuplicates INPUT=[samples/sample2/reads.sorted.bam] OUTPUT=samples/sample2/reads.sorted.deduped.bam METRICS_FILE=samples/sample2/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 614 9171 0 0 92 3 0 0.00517 14014816 jpayne@0: jpayne@0: ## HISTOGRAM java.lang.Double jpayne@0: BIN VALUE jpayne@0: 1.0 1 jpayne@0: 2.0 1.999346 jpayne@0: 3.0 2.998038 jpayne@0: 4.0 3.996077 jpayne@0: 5.0 4.993463 jpayne@0: 6.0 5.990196 jpayne@0: 7.0 6.986278 jpayne@0: 8.0 7.981707 jpayne@0: 9.0 8.976486 jpayne@0: 10.0 9.970614 jpayne@0: 11.0 10.964091 jpayne@0: 12.0 11.956919 jpayne@0: 13.0 12.949097 jpayne@0: 14.0 13.940626 jpayne@0: 15.0 14.931507 jpayne@0: 16.0 15.921739 jpayne@0: 17.0 16.911324 jpayne@0: 18.0 17.900261 jpayne@0: 19.0 18.888551 jpayne@0: 20.0 19.876195 jpayne@0: 21.0 20.863193 jpayne@0: 22.0 21.849545 jpayne@0: 23.0 22.835252 jpayne@0: 24.0 23.820314 jpayne@0: 25.0 24.804731 jpayne@0: 26.0 25.788505 jpayne@0: 27.0 26.771635 jpayne@0: 28.0 27.754122 jpayne@0: 29.0 28.735966 jpayne@0: 30.0 29.717168 jpayne@0: 31.0 30.697728 jpayne@0: 32.0 31.677647 jpayne@0: 33.0 32.656924 jpayne@0: 34.0 33.635561 jpayne@0: 35.0 34.613558 jpayne@0: 36.0 35.590915 jpayne@0: 37.0 36.567633 jpayne@0: 38.0 37.543712 jpayne@0: 39.0 38.519152 jpayne@0: 40.0 39.493954 jpayne@0: 41.0 40.468118 jpayne@0: 42.0 41.441646 jpayne@0: 43.0 42.414536 jpayne@0: 44.0 43.38679 jpayne@0: 45.0 44.358408 jpayne@0: 46.0 45.32939 jpayne@0: 47.0 46.299737 jpayne@0: 48.0 47.269449 jpayne@0: 49.0 48.238527 jpayne@0: 50.0 49.206971 jpayne@0: 51.0 50.174782 jpayne@0: 52.0 51.141959 jpayne@0: 53.0 52.108504 jpayne@0: 54.0 53.074417 jpayne@0: 55.0 54.039697 jpayne@0: 56.0 55.004346 jpayne@0: 57.0 55.968364 jpayne@0: 58.0 56.931752 jpayne@0: 59.0 57.894509 jpayne@0: 60.0 58.856637 jpayne@0: 61.0 59.818135 jpayne@0: 62.0 60.779004 jpayne@0: 63.0 61.739244 jpayne@0: 64.0 62.698857 jpayne@0: 65.0 63.657841 jpayne@0: 66.0 64.616198 jpayne@0: 67.0 65.573929 jpayne@0: 68.0 66.531033 jpayne@0: 69.0 67.48751 jpayne@0: 70.0 68.443362 jpayne@0: 71.0 69.398589 jpayne@0: 72.0 70.353191 jpayne@0: 73.0 71.307168 jpayne@0: 74.0 72.260522 jpayne@0: 75.0 73.213252 jpayne@0: 76.0 74.165358 jpayne@0: 77.0 75.116842 jpayne@0: 78.0 76.067703 jpayne@0: 79.0 77.017942 jpayne@0: 80.0 77.96756 jpayne@0: 81.0 78.916556 jpayne@0: 82.0 79.864931 jpayne@0: 83.0 80.812687 jpayne@0: 84.0 81.759822 jpayne@0: 85.0 82.706337 jpayne@0: 86.0 83.652234 jpayne@0: 87.0 84.597512 jpayne@0: 88.0 85.542171 jpayne@0: 89.0 86.486212 jpayne@0: 90.0 87.429636 jpayne@0: 91.0 88.372442 jpayne@0: 92.0 89.314632 jpayne@0: 93.0 90.256206 jpayne@0: 94.0 91.197163 jpayne@0: 95.0 92.137505 jpayne@0: 96.0 93.077232 jpayne@0: 97.0 94.016344 jpayne@0: 98.0 94.954842 jpayne@0: 99.0 95.892726 jpayne@0: 100.0 96.829996 jpayne@0: