Entering edit mode
3.6 years ago
shiy05
▴
30
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?