## htsjdk.samtools.metrics.StringHeader
# picard.sam.markduplicates.MarkDuplicates INPUT=[/oicr/data/archive/seqware/seqware_analysis_12/hsqwprod/seqware-results/BwaMem_1.2/75319535/SWID_13766179_GLCS_0001_Lv_R_PE_279_WG_DKT3-6_190305_M00146_0024_000000000-D5N29_GTCGTAGA_L001_001.annotated.bam] OUTPUT=/dev/stdout METRICS_FILE=/u/slazic/private/2019-04-22-MiSeq_precition_of_NovaSeq_Runs/picard_results/GLCS_0001_Lv_R_PE_279_WG|1|190305_M00146_0024_000000000-D5N29.txt OPTICAL_DUPLICATE_PIXEL_DISTANCE=100    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 REMOVE_DUPLICATES=false 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> VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Apr 22 14:42:04 EDT 2019

## 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
GLCS_0001_Lv_R_PE_279_WG	100	12624	1292	136	8	73	73	0.006075