process_dedup

Purpose: Mark duplicated reads, PCR or optical duplicates

Input: bam file

Outputs for later processes: dedup_bam dedup.bai stats

Process: picard ${markdup_java_options} MarkDuplicates \ INPUT=bam, \ OUTPUT=markDups.bam \ METRICS_FILE=markDups_metrics.txt \ REMOVE_DUPLICATES=true \ ASSUME_SORTED=true \ PROGRAM_RECORD_ID='null' \ VALIDATION_STRINGENCY=LENIENT

samtools index .markDups.bam

Tools: Picard Samtools