Picard - Mark Duplicates

This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.

Location

• Filepath: <SnakeLines_dir>/rules/shared/mapping/postprocess/deduplicated/picard.snake
• Rule name: picard__mark_duplicates

Input(s):

• bam: Mapped reads in bam format
• bai: Index to mapped reads for enable fast read retrieval from desired genomic region

Output(s):

• bam: Mapped reads with additional attribute that marks if read is PCR duplicate