VG - Verifying presence or absence of variants in Pangenome Graph

Question

[nkls063408]

Hi all,

I’m working with a population VCF from HGDP that contains many variations across different populations and individuals. To build a pangenome for a single population, I subsetted the VCF to include only the individuals I’m interested in. However, I noticed that the subsetted VCF still contains variants that none of my selected individuals carry (i.e., all have ./. or 0/0 in the GT field), likely because those variants were present in populations that I excluded.

My question is: I used vg autoindex to build a pangenome from this subsetted VCF (with success). I want to ensure that these excluded variants do not appear in the resulting pangenome. In theory, they shouldn’t, but is there a way to verify this? Specifically, how can I check my .xg or .gcsa files to confirm that these variants do not create "bubbles" or paths in the pangenome?

Thanks for your help!

Cheers!

Answer 1

[Jordan M Eizenga]

The behavior in vg is not what you expected it to be. All of the variants will be included, regardless of the genotypes in your samples. If you want to exclude homozygous reference calls, you should do that with bcftools before providing the VCF to vg.

[nkls063408]

I see, I didn’t expect that.. thanks for the insight. Is there a way I can visualise this? For instance, if I have a mutation where all my subsetted individuals have "./." as the genotype chromosome 1, position 100, how could I "see" this? I’m working on an HPC environment, so I don’t have access to a visual interface to use vg view. Thanks a lot !!

[Jordan M Eizenga]

If you extract a small region around a path position, you can use vg view to convert it into GFA format, which is text-based and reasonably readable for small graphs. For your example, it would look something like this:

vg chunk -p chr1:100 -c 3 -x graph.vg | vg view -