gravatar for shiy05

2 hours ago by

Dear all,

I am used to using vcftools to remove non-variants sites. The command I used:

vcftools --vcf input.vcf --mac 1 --recode --out input.mac

However, I cannot find the same command in bcftools.

I tried

bcftools view -m2 -M2 -v snps input.vcf

and

bcftools view --min-ac=1 input.vcf

All these commands keep more variants then I need, for example, the snp with all alternative genotypes 1/1.

However, I am able to get correct results using below command:

bcftools view --min-ac=1 -Q 0.9999 input.vcf

Any better suggestions?

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modified 1 hour ago

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2 hours ago
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shiy050



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