## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2012-10-20/US_Wis_Cro_1_2012-10-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2012-10-20/US_Wis_Cro_1_2012-10-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2012-10-20/US_Wis_Cro_1_2012-10-20.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 18:17:58 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 540095 33607548 0 0 143148 376061 0 0.013213 1490484011 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 32567646 32567646 2.0 1.977704 82538 82538 3.0 2.93361 6518 6518 4.0 3.868203 1351 1351 5.0 4.781958 572 572 6.0 5.675341 328 328 7.0 6.548805 257 257 8.0 7.402794 174 174 9.0 8.237743 162 162 10.0 9.054076 105 105 11.0 9.852209 93 93 12.0 10.632546 71 71 13.0 11.395485 66 66 14.0 12.141414 58 58 15.0 12.870712 60 60 16.0 13.58375 47 47 17.0 14.280889 50 50 18.0 14.962486 46 46 19.0 15.628886 40 40 20.0 16.280428 35 35 21.0 16.917443 39 39 22.0 17.540256 43 43 23.0 18.149182 39 39 24.0 18.744532 25 25 25.0 19.326609 41 41 26.0 19.895707 31 31 27.0 20.452117 30 30 28.0 20.996121 23 23 29.0 21.527997 26 26 30.0 22.048013 17 17 31.0 22.556436 26 26 32.0 23.053523 18 18 33.0 23.539527 8 8 34.0 24.014695 11 11 35.0 24.479269 19 19 36.0 24.933485 6 6 37.0 25.377574 15 15 38.0 25.811761 11 11 39.0 26.236268 14 14 40.0 26.65131 9 9 41.0 27.057099 6 6 42.0 27.45384 7 7 43.0 27.841735 12 12 44.0 28.220983 11 11 45.0 28.591774 8 8 46.0 28.954298 6 6 47.0 29.30874 5 5 48.0 29.655279 7 7 49.0 29.994092 4 4 50.0 30.325351 6 6 51.0 30.649224 5 5 52.0 30.965876 3 3 53.0 31.275468 6 6 54.0 31.578157 4 4 55.0 31.874098 3 3 56.0 32.16344 4 4 57.0 32.446332 4 4 58.0 32.722916 6 6 59.0 32.993333 7 7 60.0 33.257721 2 2 61.0 33.516215 7 7 62.0 33.768945 4 4 63.0 34.016041 4 4 64.0 34.257627 5 5 65.0 34.493827 2 2 66.0 34.72476 0 0 67.0 34.950545 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