Merge multiple vcfs vgtools

Question

[arunkumarramrsh]

Hi, Is it possible to combine vcfs produced by vg tools, all mapped using the same variant graph? Simply using bcftools etc does not seem to work since the reference calls differ.

Answer 1

[glenn.hickey]

The -a option can now be used with vg call to add reference calls: https://github.com/vgteam/vg/pull/2966

vg call -a ... -s sample1 > sample1.vcf
vg call -a ... -s sample2 > sample2.vcf

etc.

Then bcftools merge sample1.vcf.gz sample2.vcf.gz -m all to make the combined VCF.

Answer 2

[glenn.hickey]

This only works right now in "genotyping mode", where you construct a graph from a VCF with vg construct -a then genotype that same VCF with vg call -v.

I'm hoping to have a solution for general graphs, in the form of an option that makes vg call call every site with consistent positions no matter what, within the next week or so. It's coming up as a problem for many people.