This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Exclude sites on the basis of the proportion of missing data using BCFTOOLS

I want to do something very simple. I want to keep sites that do not have any missing genotypes (i.e. 100% present across all samples).

In vcftools I usually do --max-missing 1.0 as indicated in the manual, but I want to use BCFTOOLS as it is much quicker. However, I cannot find the equivalent flag to do this. I have only found F_MISSING, which I think removes individuals and not sites.

genome vcf vcftools bcftools
• 5,481 views • link
written by GabrielMontenegro GabrielMontenegro

1 answer 

$ bcftools view -e 'GT[*] = "mis"' multi-sample.vcf

This would exclude sites where any genotype is missing.

• 0 views • link
written by finswimmer finswimmer

Log in to answer this question.

More posts like this