Question

how to calculate %of missing genotype in vcf file

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2.3 years ago

rheab1230 ▴ 140

Hello, I have a vcf file which has missing genotype for certain samples. I want to find % of missing genotype in my vcf file overall. Does anyone know any software which can give me the percentage? Thank you.

vcf imputation michigan genotype • 1.5k views

ADD COMMENT • link updated 2.3 years ago by William ★ 5.3k • written 2.3 years ago by rheab1230 ▴ 140

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Duplicate of How to determine percentage missing genotypes in VCF/BCF?

ADD REPLY • link 2.3 years ago by William ★ 5.3k

score 0 · Answer 1 · 2022-09-14

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2.3 years ago

4galaxy77 2.9k

plink2 --vcf in.vcf --missing

ADD COMMENT • link 2.3 years ago by 4galaxy77 2.9k

score 0 · Answer 2 · 2022-09-14

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2.3 years ago

Pierre Lindenbaum 164k

bcftools https://samtools.github.io/bcftools/howtos/plugin.fill-tags.html

INFO/F_MISSING Number:1  Type:Float    ..  Fraction of missing genotypes (all samples, experimental)

ADD COMMENT • link 2.3 years ago by Pierre Lindenbaum 164k