The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 2019.
Filtering out M2 Mutect Calls made in regions where only 1 type of read orientation is dominant
I have applied filter criteria based on OxoG as discussed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616734/. However, I have regions that are present consistently across samples (and cancers) that have reads either in the forward direction or reverse. And also these transversions are different from what is discussed in the above paper (for transversions, C>A/G>T ).
How do I go about informatically removing these positions from my call set?
Thank you for your input!
PS, My dataset comes from WES T/N data.