## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/PL_War_Brz_1_2017-08-20/PL_War_Brz_1_2017-08-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/PL_War_Brz_1_2017-08-20/PL_War_Brz_1_2017-08-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/PL_War_Brz_1_2017-08-20/PL_War_Brz_1_2017-08-20.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: Wed Jan 18 04:25:38 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 2917693 28734507 0 0 1612904 9628473 258413 0.345603 33139598 ## HISTOGRAM java.lang.Double BIN VALUE all_sets optical_sets non_optical_sets 1.0 1.005705 12201746 0 12312234 2.0 1.428281 4239467 251636 4209562 3.0 1.605839 1400696 3046 1359850 4.0 1.680445 441947 57 419001 5.0 1.711793 135622 11 125133 6.0 1.724964 41734 3 37796 7.0 1.730499 13014 4 11457 8.0 1.732824 4202 4 3682 9.0 1.733801 1485 4 1314 10.0 1.734212 609 2 536 11.0 1.734385 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