Deduper - A Reference Based PCR Duplicate Removal Tool

Given a sorted SAM file of uniquely mapped reads, this program will remove all PCR duplicates, retaining only a single copy of each read. PCR duplicates will have the same UMI and start position (after correcting for soft clipping) on the same chromosome and strand.

Input

1. SAM file sorted by chromosome/position (samtools sort)
2. Text file with a list of UMIs (will assume random UMIs if file not provided)

• argparse options:
  • -f, --file: required arg, absolute file path of SAM file
  • -p, --paired: optional arg, designates file is paired end (not yet implemented)
  • -u, --umi: optional arg, designates file containing the list of UMIs (unset if randomers instead of UMIs)
  • -q, --quality: optional arg, will output duplicate read of highest average quality (if unset, will output first duplicate encountered)

Output

1. SAM file with PCR duplicates removed
   • {filename}_deduped.sam
2. Summary statistics
   • number of dups removed
   • number of reads with invalid UMIs
   • number of unique reads per chromosome