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Exclude sites on the basis of the proportion of missing data using BCFTOOLS
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Entering edit mode
14 months ago
United Kingdom

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.

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3
Entering edit mode
4 months ago
Germany
$ bcftools view -e 'GT[*] = "mis"' multi-sample.vcf

This would exclude sites where any genotype is missing.

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