## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Fif_Dai_1_2015-08-19/GB_Fif_Dai_1_2015-08-19.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Fif_Dai_1_2015-08-19/GB_Fif_Dai_1_2015-08-19.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Fif_Dai_1_2015-08-19/GB_Fif_Dai_1_2015-08-19.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 09:06:47 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 12870944 34867603 0 0 5353430 4578790 0 0.175665 120862388 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 25913169 25913169 2.0 1.749394 3466887 3466887 3.0 2.310986 429463 429463 4.0 2.731839 52036 52036 5.0 3.047225 6802 6802 6.0 3.283573 1381 1381 7.0 3.46069 609 609 8.0 3.593421 372 372 9.0 3.692889 285 285 10.0 3.76743 251 251 11.0 3.82329 169 169 12.0 3.865152 160 160 13.0 3.896522 145 145 14.0 3.920031 120 120 15.0 3.937649 105 105 16.0 3.950851 84 84 17.0 3.960745 80 80 18.0 3.968159 65 65 19.0 3.973716 65 65 20.0 3.97788 46 46 21.0 3.981 53 53 22.0 3.983338 50 50 23.0 3.985091 39 39 24.0 3.986404 29 29 25.0 3.987388 27 27 26.0 3.988126 21 21 27.0 3.988678 37 37 28.0 3.989092 29 29 29.0 3.989403 25 25 30.0 3.989635 22 22 31.0 3.98981 20 20 32.0 3.98994 24 24 33.0 3.990038 18 18 34.0 3.990112 14 14 35.0 3.990167 20 20 36.0 3.990208 15 15 37.0 3.990239 17 17 38.0 3.990262 14 14 39.0 3.990279 8 8 40.0 3.990292 17 17 41.0 3.990302 13 13 42.0 3.990309 15 15 43.0 3.990315 14 14 44.0 3.990319 9 9 45.0 3.990322 8 8 46.0 3.990324 15 15 47.0 3.990326 7 7 48.0 3.990327 3 3 49.0 3.990328 8 8 50.0 3.990329 6 6 51.0 3.990329 3 3 52.0 3.99033 7 7 53.0 3.99033 5 5 54.0 3.99033 3 3 55.0 3.99033 6 6 56.0 3.990331 10 10 57.0 3.990331 1 1 58.0 3.990331 6 6 59.0 3.990331 16 16 60.0 3.990331 3 3 61.0 3.990331 8 8 62.0 3.990331 4 4 63.0 3.990331 3 3 64.0 3.990331 4 4 65.0 3.990331 2 2 66.0 3.990331 3 3 67.0 3.990331 5 5 68.0 3.990331 4 4 69.0 3.990331 0 0 70.0 3.990331 2 2 71.0 3.990331 9 9 72.0 3.990331 3 3 73.0 3.990331 3 3 74.0 3.990331 5 5 75.0 3.990331 6 6 76.0 3.990331 3 3 77.0 3.990331 3 3 78.0 3.990331 2 2 79.0 3.990331 3 3 80.0 3.990331 2 2 81.0 3.990331 3 3 82.0 3.990331 1 1 83.0 3.990331 6 6 84.0 3.990331 4 4 85.0 3.990331 2 2 86.0 3.990331 1 1 87.0 3.990331 2 2 88.0 3.990331 3 3 89.0 3.990331 1 1 90.0 3.990331 1 1 91.0 3.990331 3 3 92.0 3.990331 1 1 93.0 3.990331 2 2 94.0 3.990331 1 1 95.0 3.990331 0 0 96.0 3.990331 2 2 97.0 3.990331 1 1 98.0 3.990331 0 0 99.0 3.990331 0 0 100.0 3.990331 2 2 101.0 0 3 3 102.0 0 1 1 103.0 0 2 2 105.0 0 1 1 106.0 0 1 1 107.0 0 1 1 114.0 0 4 4 116.0 0 1 1 117.0 0 1 1 118.0 0 2 2 119.0 0 1 1 123.0 0 1 1 127.0 0 1 1 128.0 0 1 1 131.0 0 1 1 134.0 0 3 3 138.0 0 2 2 140.0 0 1 1 141.0 0 1 1 143.0 0 1 1 150.0 0 1 1 153.0 0 1 1 157.0 0 1 1 173.0 0 1 1 177.0 0 1 1 182.0 0 1 1 189.0 0 1 1 193.0 0 1 1 201.0 0 1 1 204.0 0 2 2 207.0 0 1 1 248.0 0 1 1 254.0 0 1 1 293.0 0 1 1 297.0 0 1 1 392.0 0 1 1 434.0 0 1 1 456.0 0 1 1 578.0 0 1 1