filtering VCF sites and impose whatever excluded ad missing

Question

[Matteo Ungaro]

Hi there I have several individual VCF files on which I'm working on to retain calls with only a depth greater than 10 and a genotype quality greater than 30. Also, I'm preserving missing sites.

However, I wonder if there is a way to set the condition so that every site excluded from the previous filters e.g. MIN(FMT/DP)>10 & MIN(FMT/GQ)>30 can be set as missing. Below the exact command I used:

bcftools view --threads 32 -i 'MIN(FMT/DP)>10 & MIN(FMT/GQ)>30 | GT[*]="mis"' -R chromosome.list $d/output/${ID}.vcf.gz -Oz -o $d/output/${ID}_filtered.vcf.gz

Let me know, thanks in advance!

Answer 1

[Pierre Lindenbaum]

not sure about your query but you could play with bcftools +setGT

bcftools +setGT in.vcf.gz -- -t q -n . -i 'FORMAT/DP<10 || FORMAT/GQ < 30'

[Matteo Ungaro]

@Pierre Lindenbaum I'm not familiar with +setGT... what is meant to do? Also, you mean the query I need is not easily doable just by using bcftools?

[Pierre Lindenbaum]

I'm not familiar with +setGT...

https://samtools.github.io/bcftools/howtos/plugins.html

[Matteo Ungaro]

Oh I see, I think I got it. However, this will require to first run the command you shared, and then run what I was using on top, is that the case? If so, would there be a way to do it in one command; not that it is strictly necessary but just form my understanding. Thanks again!