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Return reference calls with `vg calls`

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5.4 years ago

Felix Bemm ▴ 20

How would one call reference bases withvg call at the moment as such that they appear as 0/0 if read alignments support it?vg call had an option in 1.17 if I remember correctly but that disappeared in 1.19, Wouldvg genotype be one way?

Thanks,Felix

vg vgteam • 1.4k views

ADD COMMENT •link 5.3 years ago by Felix Bemm ▴ 20

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Please edit your question so users (which are apparently not vg-Team) would be able to help you.

ADD REPLY •link 5.4 years ago by Asaf 10k

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I think in this case only the vg team can help me.

ADD REPLY •link 5.4 years ago by Felix Bemm ▴ 20

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I am running genotype like that:

./vg genotype -p -t 20 -v -r "path1" -V sample.vcf -E -G sample.fil.gam sample.aug.vg > sample.recall.vcf

sample.vcf is from vg callsample.fil.gam is an augmented filtered gamsample.aug.vg is the augmented graph

vg genotype works but the process takes huge amounts of memory for a pretty small graph.The graph is not from the vcf, its a genome alignment graph.

And it seems as genotype is not adding the path id to the vcf header.

ADD REPLY •link 5.3 years ago by Felix Bemm ▴ 20

score 1 · Answer 1 · 2019-11-27

Yeah, that option got lost when vg call was refactored (it didn't work very well). Please file a github issue to ask for it back.

But vg callcan genotype a given VCF with the -v option, if the graph was constructed from that VCF with vg construct -a. This will produce 0/0 calls.