## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Uma_7_Oct_2017/UA_Uma_7_Oct_2017.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Uma_7_Oct_2017/UA_Uma_7_Oct_2017.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Uma_7_Oct_2017/UA_Uma_7_Oct_2017.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 Dec 21 04:06:19 UTC 2022 ## 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 3659806 16674663 0 0 1709090 5035383 140791 0.318296 22088576 ## HISTOGRAM java.lang.Double BIN VALUE all_sets optical_sets non_optical_sets 1.0 1.005704 7810378 0 7879791 2.0 1.478443 2406011 136886 2379553 3.0 1.700658 684764 1449 659702 4.0 1.805111 184360 39 172635 5.0 1.85421 47925 13 43760 6.0 1.87729 12901 10 11530 7.0 1.888139 3778 6 3353 8.0 1.893238 1394 6 1267 9.0 1.895635 668 5 620 10.0 1.896762 422 2 412 11.0 1.897292 324 4 316 12.0 1.897541 252 3 255 13.0 1.897658 200 2 196 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