exomeAdvancedVariantFiltering

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

Details on input and output:

Input:

1. mutfile - *R.mutations file containing processed variant calls for patient
2. (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

Output:

1. (not returned) mutavffile - *R.mutations.avf file updated with flags and decisions