## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/AU_Tas_Tas_1_2004-07-01/AU_Tas_Tas_1_2004-07-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/AU_Tas_Tas_1_2004-07-01/AU_Tas_Tas_1_2004-07-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/AU_Tas_Tas_1_2004-07-01/AU_Tas_Tas_1_2004-07-01.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=<optimized capture of last three ':' separated fields as numeric values> 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: Thu Feb 23 18:38:01 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	15858417	0	0	0	1474743	0	0	0.092994