## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-08-27/TR_Ank_Yes_1_2015-08-27.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-08-27/TR_Ank_Yes_1_2015-08-27.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-08-27/TR_Ank_Yes_1_2015-08-27.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 09:07:23 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 15965572 32954904 0 0 6531697 5558854 0 0.215564 86359167 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 22389639 22389639 2.0 1.682766 3913813 3913813 3.0 2.148936 626213 626213 4.0 2.467221 94856 94856 5.0 2.684535 14433 14433 6.0 2.83291 2449 2449 7.0 2.934215 600 600 8.0 3.003383 306 306 9.0 3.050608 222 222 10.0 3.082852 158 158 11.0 3.104867 118 118 12.0 3.119898 89 89 13.0 3.130161 74 74 14.0 3.137168 74 74 15.0 3.141952 52 52 16.0 3.145219 52 52 17.0 3.147449 51 51 18.0 3.148972 37 37 19.0 3.150011 30 30 20.0 3.150721 32 32 21.0 3.151206 36 36 22.0 3.151537 26 26 23.0 3.151763 38 38 24.0 3.151917 16 16 25.0 3.152022 20 20 26.0 3.152094 11 11 27.0 3.152143 21 21 28.0 3.152177 12 12 29.0 3.1522 11 11 30.0 3.152215 11 11 31.0 3.152226 10 10 32.0 3.152233 15 15 33.0 3.152238 11 11 34.0 3.152242 7 7 35.0 3.152244 14 14 36.0 3.152245 8 8 37.0 3.152247 8 8 38.0 3.152247 14 14 39.0 3.152248 10 10 40.0 3.152248 4 4 41.0 3.152248 6 6 42.0 3.152249 8 8 43.0 3.152249 5 5 44.0 3.152249 8 8 45.0 3.152249 6 6 46.0 3.152249 1 1 47.0 3.152249 6 6 48.0 3.152249 7 7 49.0 3.152249 7 7 50.0 3.152249 9 9 51.0 3.152249 2 2 52.0 3.152249 5 5 53.0 3.152249 2 2 54.0 3.152249 2 2 55.0 3.152249 1 1 56.0 3.152249 3 3 57.0 3.152249 3 3 58.0 3.152249 4 4 59.0 3.152249 1 1 60.0 3.152249 1 1 61.0 3.152249 2 2 62.0 3.152249 4 4 63.0 3.152249 2 2 64.0 3.152249 5 5 65.0 3.152249 2 2 66.0 3.152249 3 3 67.0 3.152249 2 2 68.0 3.152249 1 1 69.0 3.152249 2 2 70.0 3.152249 2 2 71.0 3.152249 1 1 72.0 3.152249 3 3 73.0 3.152249 1 1 74.0 3.152249 0 0 75.0 3.152249 3 3 76.0 3.152249 3 3 77.0 3.152249 2 2 78.0 3.152249 0 0 79.0 3.152249 3 3 80.0 3.152249 0 0 81.0 3.152249 1 1 82.0 3.152249 1 1 83.0 3.152249 1 1 84.0 3.152249 1 1 85.0 3.152249 1 1 86.0 3.152249 0 0 87.0 3.152249 0 0 88.0 3.152249 0 0 89.0 3.152249 1 1 90.0 3.152249 0 0 91.0 3.152249 1 1 92.0 3.152249 0 0 93.0 3.152249 2 2 94.0 3.152249 1 1 95.0 3.152249 1 1 96.0 3.152249 1 1 97.0 3.152249 0 0 98.0 3.152249 0 0 99.0 3.152249 1 1 100.0 3.152249 0 0 102.0 0 1 1 109.0 0 1 1 110.0 0 1 1 112.0 0 1 1 115.0 0 1 1 117.0 0 1 1 122.0 0 1 1 132.0 0 2 2 134.0 0 1 1 141.0 0 1 1 144.0 0 1 1 146.0 0 1 1 151.0 0 1 1 152.0 0 1 1 153.0 0 2 2 176.0 0 1 1 180.0 0 1 1 186.0 0 1 1 190.0 0 1 1 260.0 0 1 1 324.0 0 1 1 393.0 0 1 1 431.0 0 1 1 464.0 0 1 1