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bcftools filtering only 10% missing genotype

Hello everyone,

I would like to keep only 90% of my missing genotype on all my samples. I used this option of bcftools : 

bcftools view -g ^miss  variants.vcf.gz -Oz -o filtered_variants.vcf.gz

When I use this option my variant it's deleted for all the samples. I know it's possible to use regular expressions in bcftools, but I'm a little confused.

Thank you very much.

snp sequence gene sequencing next-gen
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Sillpositive • Sillpositive

I've edited your post to a Question. The post type Tool is to advertise a new tool, not to ask questions about using tools.

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written by Emily Emily

1 answer 

bcftools view -i 'F_MISSING<0.1'  in.vcf
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written by Pierre Lindenbaum Pierre Lindenbaum

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