I successfully ran the Strelka2 germline workflow on some BAM files. That being said, I have several variant calls and I'm struggling to figure out how to calculate Minor Allele Frequency (MAF) with the outputs generated by this script. I am able to filter and select only "passing" calls and those with specific quality scores above a minimum value, plus select for calls with depths > 250x. With that, does anyone have any suggestion on how to calculate MAF? I want to filter out everything > 3% MAF. Please advise. Thank you!!
I successfully ran the Strelka2 germline workflow on some BAM files. That being said, I have several variant calls and I'm struggling to figure out how to calculate Minor Allele Frequency (MAF) with the outputs generated by this script. I am able to filter and select only "passing" calls and those with specific quality scores above a minimum value, plus select for calls with depths > 250x. With that, does anyone have any suggestion on how to calculate MAF? I want to filter out everything > 3% MAF. Please advise. Thank you!!