Amplicon Checker

Purpose: To check for amplicon coverage dropouts

Goals:

Expected inputs:

• bam file
• primer scheme file --> determine amplicons based on it
• bam files of old samples to compare against (to set regional thresholds rather than a generic constant value)

What to base thresholds on:

• exact minimum coverage threshold
• minimum coverage as a percent of sample's highest coverage regions
• observed typical coverage in region based on older data

Potential outputs:

• list of regions (based on windows) with lower than threshold coverage
• List of amplicons (based on primers) containing any dropouts (by windows)
• List of amplicons (based on primers) fully dropped out
• pass/fail boolean