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Illumina / strelka

Strelka2 germline and somatic small variant caller
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Include AD (allelic depths) in format from somatic variants #233

Closed juliawiggeshoff closed 9 months ago

juliawiggeshoff commented 11 months ago

Is it possible to include the Allelic depths for the ref and alt alleles in the order listed (AD) in the format fields from the somatic SNV and INDEL files?

It seems like this feature is available for germline variant calling, but not for somatic.

The following has been mentioned by @ctsa under issue #3:

@IraDeveson - We will add a section to the user guide for the upcoming 2.8.0 release. @student-t - "AF" is perhaps too easily confused with its population allele frequency usage, the likely trajectory is to move towards the more standard AD counts, which will make the corresponding allele frequency simpler to extract.

Originally posted by @ctsa in https://github.com/Illumina/strelka/issues/3#issuecomment-308874551

juliawiggeshoff commented 9 months ago

Originally, I requested this to be able to easily calculate VAF using bcftools +fill-tags, as I can with other callers I use, but I have since "given up" on this request and had to write my own script to calculate the VAF for the variants, as mentioned in the comment from this issue: https://github.com/Illumina/strelka/issues/234#issuecomment-1859952530

Here is the script, if anyone encounters the same problem...