## net.sf.picard.metrics.StringHeader # net.sf.picard.sam.MarkDuplicates INPUT=[HSR_sci1_K27ac.bwameth.hg38.bam] OUTPUT=HSR_sci1_K27ac.bwameth.hg38.dedup.bam METRICS_FILE=HSR_sci1_K27ac.bwameth.hg38.dedup.metric REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false ## net.sf.picard.metrics.StringHeader # Started on: Mon Mar 23 18:14:33 PDT 2026 ## METRICS CLASS net.sf.picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE 0 1314308 0 0 666846 183559 0.507374 910348 ## HISTOGRAM java.lang.Double BIN VALUE 1.0 1.074143 2.0 1.327687 3.0 1.387534 4.0 1.401661 5.0 1.404995 6.0 1.405782 7.0 1.405968 8.0 1.406012 9.0 1.406022 10.0 1.406025 11.0 1.406025 12.0 1.406025 13.0 1.406025 14.0 1.406025 15.0 1.406025 16.0 1.406025 17.0 1.406025 18.0 1.406025 19.0 1.406025 20.0 1.406025 21.0 1.406025 22.0 1.406025 23.0 1.406025 24.0 1.406025 25.0 1.406025 26.0 1.406025 27.0 1.406025 28.0 1.406025 29.0 1.406025 30.0 1.406025 31.0 1.406025 32.0 1.406025 33.0 1.406025 34.0 1.406025 35.0 1.406025 36.0 1.406025 37.0 1.406025 38.0 1.406025 39.0 1.406025 40.0 1.406025 41.0 1.406025 42.0 1.406025 43.0 1.406025 44.0 1.406025 45.0 1.406025 46.0 1.406025 47.0 1.406025 48.0 1.406025 49.0 1.406025 50.0 1.406025 51.0 1.406025 52.0 1.406025 53.0 1.406025 54.0 1.406025 55.0 1.406025 56.0 1.406025 57.0 1.406025 58.0 1.406025 59.0 1.406025 60.0 1.406025 61.0 1.406025 62.0 1.406025 63.0 1.406025 64.0 1.406025 65.0 1.406025 66.0 1.406025 67.0 1.406025 68.0 1.406025 69.0 1.406025 70.0 1.406025 71.0 1.406025 72.0 1.406025 73.0 1.406025 74.0 1.406025 75.0 1.406025 76.0 1.406025 77.0 1.406025 78.0 1.406025 79.0 1.406025 80.0 1.406025 81.0 1.406025 82.0 1.406025 83.0 1.406025 84.0 1.406025 85.0 1.406025 86.0 1.406025 87.0 1.406025 88.0 1.406025 89.0 1.406025 90.0 1.406025 91.0 1.406025 92.0 1.406025 93.0 1.406025 94.0 1.406025 95.0 1.406025 96.0 1.406025 97.0 1.406025 98.0 1.406025 99.0 1.406025 100.0 1.406025