Calculate allele frequencies

[silviamorins]

Hi,

in the first place thank you for the effort you made with Strelka and for how well it is documented. I know from here how to calculate the allele frequencies, but my .vcf files, especially those containing snvs, have a very large amount of lines, making the computation of the allele frequencies line by line not very quick - I was wondering if there is a reason why this is not already part of Strelka's output?

Thanks in advance!

[sangtaekim]

There's no strong reason, but unfortunately we do not have a plan to change the output format. Sorry for the inconvenience.

[DarioS]

The information linked to contains a formula for calculating somatic variant frequency. What about for the germline output files? I thought about dividing AD by DP, but only one of those numbers is output for each variant - never both. Like Silvia, I wish the VCF files would contain VAF by default.

[FriederikeHanssen]

some docs on computing VAF for germline samples would be great. I guess we should divide the second value from the AD list by DP?