## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2015-08-23/RU_Nov_Val_1_2015-08-23.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2015-08-23/RU_Nov_Val_1_2015-08-23.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2015-08-23/RU_Nov_Val_1_2015-08-23.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 08:43:56 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 11996036 29198233 0 0 4458884 2831754 0 0.143799 140632812 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 23513620 23513620 2.0 1.812515 2347920 2347920 3.0 2.472697 199943 199943 4.0 3.009104 16941 16941 5.0 3.444944 1875 1875 6.0 3.79907 545 545 7.0 4.086803 288 288 8.0 4.320591 179 179 9.0 4.510547 140 140 10.0 4.664889 114 114 11.0 4.790294 87 87 12.0 4.892188 67 67 13.0 4.974978 63 63 14.0 5.042247 49 49 15.0 5.096904 41 41 16.0 5.141313 32 32 17.0 5.177396 38 38 18.0 5.206714 33 33 19.0 5.230536 33 33 20.0 5.249891 28 28 21.0 5.265618 18 18 22.0 5.278396 12 12 23.0 5.288778 19 19 24.0 5.297214 13 13 25.0 5.304068 14 14 26.0 5.309637 15 15 27.0 5.314162 10 10 28.0 5.317839 12 12 29.0 5.320826 13 13 30.0 5.323254 11 11 31.0 5.325226 8 8 32.0 5.326828 7 7 33.0 5.32813 9 9 34.0 5.329188 11 11 35.0 5.330048 6 6 36.0 5.330746 7 7 37.0 5.331314 5 5 38.0 5.331775 3 3 39.0 5.332149 6 6 40.0 5.332454 5 5 41.0 5.332701 5 5 42.0 5.332902 6 6 43.0 5.333065 5 5 44.0 5.333198 3 3 45.0 5.333306 3 3 46.0 5.333393 4 4 47.0 5.333465 1 1 48.0 5.333522 5 5 49.0 5.333569 4 4 50.0 5.333608 0 0 51.0 5.333639 0 0 52.0 5.333664 3 3 53.0 5.333684 0 0 54.0 5.333701 3 3 55.0 5.333714 1 1 56.0 5.333725 2 2 57.0 5.333734 2 2 58.0 5.333742 1 1 59.0 5.333747 1 1 60.0 5.333752 2 2 61.0 5.333756 1 1 62.0 5.333759 0 0 63.0 5.333762 4 4 64.0 5.333764 0 0 65.0 5.333766 0 0 66.0 5.333767 2 2 67.0 5.333768 1 1 68.0 5.333769 0 0 69.0 5.33377 1 1 70.0 5.33377 0 0 71.0 5.333771 0 0 72.0 5.333771 0 0 73.0 5.333772 1 1 74.0 5.333772 0 0 75.0 5.333772 1 1 76.0 5.333772 1 1 77.0 5.333772 0 0 78.0 5.333772 2 2 79.0 5.333773 0 0 80.0 5.333773 0 0 81.0 5.333773 0 0 82.0 5.333773 0 0 83.0 5.333773 0 0 84.0 5.333773 0 0 85.0 5.333773 1 1 86.0 5.333773 2 2 87.0 5.333773 1 1 88.0 5.333773 0 0 89.0 5.333773 0 0 90.0 5.333773 1 1 91.0 5.333773 1 1 92.0 5.333773 1 1 93.0 5.333773 0 0 94.0 5.333773 0 0 95.0 5.333773 0 0 96.0 5.333773 0 0 97.0 5.333773 1 1 98.0 5.333773 0 0 99.0 5.333773 1 1 100.0 5.333773 0 0 109.0 0 1 1 111.0 0 1 1 112.0 0 1 1 115.0 0 1 1 118.0 0 1 1 192.0 0 1 1 204.0 0 1 1 220.0 0 1 1 246.0 0 1 1 287.0 0 1 1