Question: Exclude sites on the basis of the proportion of missing data using BCFTOOLS
0
gravatar for GabrielMontenegro
10 days ago by
United Kingdom
GabrielMontenegro520 wrote:

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.

vcftools bcftools vcf genome • 83 views
ADD COMMENTlink modified 10 days ago • written 10 days ago by GabrielMontenegro520
3
gravatar for finswimmer
10 days ago by
finswimmer11k
Germany
finswimmer11k wrote:
$ bcftools view -e 'GT[*] = "mis"' multi-sample.vcf

This would exclude sites where any genotype is missing.

ADD COMMENTlink modified 10 days ago • written 10 days ago by finswimmer11k
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