## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-09-17/TR_Ank_Yes_1_2015-09-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-09-17/TR_Ank_Yes_1_2015-09-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-09-17/TR_Ank_Yes_1_2015-09-17.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 08:37:53 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 8922214 23918925 0 0 7819394 19963425 0 0.841194 3965014 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 811142 811142 2.0 1.002399 264228 264228 3.0 1.002405 228450 228450 4.0 1.002405 245240 245240 5.0 1.002405 261119 261119 6.0 1.002405 267655 267655 7.0 1.002405 264865 264865 8.0 1.002405 251590 251590 9.0 1.002405 230829 230829 10.0 1.002405 202080 202080 11.0 1.002405 172929 172929 12.0 1.002405 141502 141502 13.0 1.002405 112652 112652 14.0 1.002405 86749 86749 15.0 1.002405 64605 64605 16.0 1.002405 46700 46700 17.0 1.002405 33262 33262 18.0 1.002405 22381 22381 19.0 1.002405 15009 15009 20.0 1.002405 9825 9825 21.0 1.002405 6174 6174 22.0 1.002405 3971 3971 23.0 1.002405 2479 2479 24.0 1.002405 1549 1549 25.0 1.002405 914 914 26.0 1.002405 521 521 27.0 1.002405 356 356 28.0 1.002405 210 210 29.0 1.002405 137 137 30.0 1.002405 81 81 31.0 1.002405 50 50 32.0 1.002405 21 21 33.0 1.002405 20 20 34.0 1.002405 24 24 35.0 1.002405 14 14 36.0 1.002405 12 12 37.0 1.002405 7 7 38.0 1.002405 9 9 39.0 1.002405 5 5 40.0 1.002405 7 7 41.0 1.002405 3 3 42.0 1.002405 7 7 43.0 1.002405 5 5 44.0 1.002405 2 2 45.0 1.002405 2 2 46.0 1.002405 3 3 47.0 1.002405 4 4 48.0 1.002405 6 6 49.0 1.002405 4 4 50.0 1.002405 3 3 51.0 1.002405 0 0 52.0 1.002405 0 0 53.0 1.002405 1 1 54.0 1.002405 2 2 55.0 1.002405 1 1 56.0 1.002405 0 0 57.0 1.002405 2 2 58.0 1.002405 2 2 59.0 1.002405 0 0 60.0 1.002405 0 0 61.0 1.002405 4 4 62.0 1.002405 1 1 63.0 1.002405 1 1 64.0 1.002405 2 2 65.0 1.002405 0 0 66.0 1.002405 0 0 67.0 1.002405 2 2 68.0 1.002405 0 0 69.0 1.002405 3 3 70.0 1.002405 2 2 71.0 1.002405 0 0 72.0 1.002405 1 1 73.0 1.002405 1 1 74.0 1.002405 0 0 75.0 1.002405 1 1 76.0 1.002405 0 0 77.0 1.002405 0 0 78.0 1.002405 0 0 79.0 1.002405 2 2 80.0 1.002405 1 1 81.0 1.002405 0 0 82.0 1.002405 2 2 83.0 1.002405 0 0 84.0 1.002405 0 0 85.0 1.002405 0 0 86.0 1.002405 0 0 87.0 1.002405 1 1 88.0 1.002405 0 0 89.0 1.002405 1 1 90.0 1.002405 0 0 91.0 1.002405 0 0 92.0 1.002405 2 2 93.0 1.002405 1 1 94.0 1.002405 1 1 95.0 1.002405 0 0 96.0 1.002405 0 0 97.0 1.002405 0 0 98.0 1.002405 1 1 99.0 1.002405 0 0 100.0 1.002405 0 0 102.0 0 1 1 112.0 0 1 1 118.0 0 1 1 119.0 0 1 1 121.0 0 1 1 128.0 0 1 1 130.0 0 1 1 131.0 0 1 1 134.0 0 1 1 137.0 0 1 1 138.0 0 1 1 151.0 0 1 1 154.0 0 1 1 156.0 0 1 1 168.0 0 1 1 175.0 0 1 1 189.0 0 1 1 207.0 0 1 1 208.0 0 1 1 251.0 0 1 1 269.0 0 1 1 357.0 0 1 1 393.0 0 1 1 628.0 0 1 1 635.0 0 1 1