Include VAF in the output

[QichenFU]

Hi, may I ask if SVDSS could include VAF in the output VCF file?

[ldenti]

Hi, sorry for the late reply. I think the easiest way to achieve this is:

1. run SVDSS
2. genotype the output VCF using e.g. kanpig
3. run bcftools to include the VAF

bcftools +fill-tags SVDSS2-q0.98-w2.vcf.gz -- -t VAF

I'm currently working on SVDSS v2.1.0 and I'm trying to automate these three steps but it may require some time.

Let me know if this might do what you need.