Variant Allele Frequency

Question

[adarsh_pp]

How do we interpret the variant allele frequency to understand whether the variant is germline or somatic? How is it actually calculated?

I googled for these, but could not find a satisfactory answer.

Please help me, Thanks

[German.M.Demidov]

if you have a homogeneous tumor (without sub-clones) that is 100% pure (has no normal cells sequenced together) your allele frequency will be perfectly around 0.5 and 1 (OK this one is rare) - as for germline. In general (as Emily_Ensembl said) you need normal tissue and subtract normal mutations from tumor mutations.

Answer 1

[Emily]

A somatic variant is identified by calling the cancer tissue compared to a non-cancerous tissue. It has nothing to do with frequency.