Case Control count per variant

Question

[williamsbrian5064]

Hi,

I was wonder if there was any software out there that will count the number of samples in a group that are homozygous ref, heterozygous, or homozygous for a variant an output result in a text file? In the past, I have been able to count the number of samples in a group that are homozygous ref, heterozygous, or homozygous, but I have done this using SnpEff and R. I did this by having SnpEff show the genotype of each sample and then used R to count up the sample base on the SnpEff genotype information. Overall this method is slow and can be messy at times. I was wondering if there was any software out there that did this for you? I tried looking around the forum to see if anyone else had asked this question, but I couldn't find much. I also could have been using the wrong search terms.

Thanks in advance

[Pierre Lindenbaum]

duplicate: Which tool to calculate per site stats on vcf file?

[williamsbrian5064]

Does the bcftools plugin work for multiple groups?

[Pierre Lindenbaum]

use bcftools view --samples xxx in.vcf for each group, pipe it in the tool and then paste the results for eacg group.

[williamsbrian5064]

Awesome! I will give that a try