A post-mutation calling pipeline for additional variant filtering.
To use, clone repository to the desired directory, then run with:
python advanced_variant_filtering.py mutfile
- mutfile - *R.mutations file containing processed variant calls for patient
- (not directly input with run command but required in same directory as mutfile) quality stats file - *.qualitystats.txt file generated by the running my exomeQualityPlots; see start of advanced_variant_filtering.py for more info on how it is used
- (not returned) mutavffile - *R.mutations.avf file updated with flags and decisions