SN reads duplicated: 8294174 # PCR or optical duplicate bit set SN reads paired: 38228224 # paired-end technology bit set SN reads properly paired: 31370896 # proper-pair bit set SN reads mapped and paired: 32441118 # paired-end technology bit set + both mates mapped INPUT= OUTPUT=L002_full_Pv.marked_dups.bam METRICS_FILE=L002_full_Pv.marked_dups_metrics.txt ASSUME_SORTED=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_DUPLICATES=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=+::(+):(+):(+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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 INPUT=L002_full_Pv.cleaned.sam OUTPUT=L002_full_Pv.sorted.bam SORT_ORDER=coordinate 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 INPUT=L002_full_Pv.cleaned.sam ASSUME_SORTED=false ADD_MATE_CIGAR=true IGNORE_MISSING_MATES=true 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 INPUT=L002_full_Pv.sam OUTPUT=L002_full_Pv.cleaned.sam 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 usr/local/packages/bwa-0.7.13/bin/bwa mem -M -R /local/scratch/sagrawal/ReferenceGenomes/Pvivax/PlasmoDB-28_PvivaxSal1_Genome.indexed L002_R1_ L002_R2_
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