bcftools to remove non-variants sites

Question

[shiy05]

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?

Answer 1

[shiy05]

I find out my answer:

bcftools view -c 1 -c 1:nonmajor test.vcf
#or
bcftools view -i "MAC >=1" test.vcf  #make sure you have only biallelic sites
#or
bcftools filter -e "MAC == 0" test.vcf #make sure you have only biallelic sites

However, if your %INFO tags is wrong, bcftools will produce error results.