I want to know if there is a way to keep sites with 0% missing a VCF file.
On vcftools I can do:
vcftools --vcf input_file.vcf --max-missing 1.0 --out output_noMissing
Is there a way to do this with BCFTOOLS as it is much faster?
bcftools view -g ^miss input.vcf
$ bcftools view -e 'GT[*]="mis"' input.vcf
This will exclude (-e) sites where any genotype (GT[*]) is missing (="mis").
bcftools filter --include 'AN=2*N_SAMPLES' [VCF/BCF]
[courtesy finswimmer for N_SAMPLES part]
Pierre's, finswimmer's, and this solution all produce the exact same output (tested with diff)
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