## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_6_2015-08-26/UA_Kie_Cho_6_2015-08-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_6_2015-08-26/UA_Kie_Cho_6_2015-08-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_6_2015-08-26/UA_Kie_Cho_6_2015-08-26.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT 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 DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true 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 VERBOSITY=INFO QUIET=false 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 ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Jan 20 17:23:40 UTC 2023 ## METRICS CLASS picard.sam.DuplicationMetrics 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 lib1 12480382 33091850 0 0 5109468 4124403 0 0.169814 121478660 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 24999728 24999728 2.0 1.761543 3201363 3201363 3.0 2.341491 370695 370695 4.0 2.783146 41907 41907 5.0 3.119485 5050 5050 6.0 3.375622 957 957 7.0 3.570681 381 381 8.0 3.719227 246 246 9.0 3.832351 166 166 10.0 3.918499 163 163 11.0 3.984106 112 112 12.0 4.034067 74 74 13.0 4.072115 78 78 14.0 4.101091 75 75 15.0 4.123157 68 68 16.0 4.139961 43 43 17.0 4.152758 55 55 18.0 4.162503 36 36 19.0 4.169925 35 35 20.0 4.175577 32 32 21.0 4.179881 31 31 22.0 4.183159 29 29 23.0 4.185655 9 9 24.0 4.187556 12 12 25.0 4.189003 18 18 26.0 4.190106 20 20 27.0 4.190945 16 16 28.0 4.191585 21 21 29.0 4.192072 22 22 30.0 4.192443 15 15 31.0 4.192725 14 14 32.0 4.19294 17 17 33.0 4.193104 18 18 34.0 4.193228 7 7 35.0 4.193323 11 11 36.0 4.193396 5 5 37.0 4.193451 8 8 38.0 4.193493 9 9 39.0 4.193525 12 12 40.0 4.193549 8 8 41.0 4.193568 7 7 42.0 4.193582 6 6 43.0 4.193592 1 1 44.0 4.193601 3 3 45.0 4.193607 7 7 46.0 4.193612 4 4 47.0 4.193615 0 0 48.0 4.193618 1 1 49.0 4.19362 5 5 50.0 4.193622 7 7 51.0 4.193623 5 5 52.0 4.193624 2 2 53.0 4.193624 4 4 54.0 4.193625 3 3 55.0 4.193625 2 2 56.0 4.193626 1 1 57.0 4.193626 0 0 58.0 4.193626 2 2 59.0 4.193626 0 0 60.0 4.193626 1 1 61.0 4.193626 0 0 62.0 4.193627 3 3 63.0 4.193627 1 1 64.0 4.193627 1 1 65.0 4.193627 5 5 66.0 4.193627 2 2 67.0 4.193627 2 2 68.0 4.193627 2 2 69.0 4.193627 0 0 70.0 4.193627 2 2 71.0 4.193627 2 2 72.0 4.193627 0 0 73.0 4.193627 1 1 74.0 4.193627 1 1 75.0 4.193627 1 1 76.0 4.193627 0 0 77.0 4.193627 1 1 78.0 4.193627 2 2 79.0 4.193627 0 0 80.0 4.193627 1 1 81.0 4.193627 0 0 82.0 4.193627 0 0 83.0 4.193627 2 2 84.0 4.193627 3 3 85.0 4.193627 0 0 86.0 4.193627 0 0 87.0 4.193627 0 0 88.0 4.193627 0 0 89.0 4.193627 1 1 90.0 4.193627 0 0 91.0 4.193627 1 1 92.0 4.193627 1 1 93.0 4.193627 0 0 94.0 4.193627 0 0 95.0 4.193627 0 0 96.0 4.193627 0 0 97.0 4.193627 0 0 98.0 4.193627 0 0 99.0 4.193627 0 0 100.0 4.193627 0 0 103.0 0 1 1 107.0 0 1 1 111.0 0 1 1 119.0 0 1 1 121.0 0 1 1 125.0 0 1 1 126.0 0 1 1 130.0 0 1 1 151.0 0 1 1 163.0 0 1 1 173.0 0 1 1 177.0 0 1 1 306.0 0 1 1 328.0 0 1 1