A method to count genotype ALT amounts for a vcf file with 3 samples?
0
0
Entering edit mode
7 months ago
kadamek49 • 0

Hello,

I have a vcf file with 3 different samples that are compared to the reference genome. I am looking for a way to count the ALT genotypes that appear for each sample. But I would like to take this a step further by using some code to look into the accumulating variants. Thus, I would like to view counts of ALTs genotypes appearing in sample 1 + 2, and sample 1+2+3. I am currently looking into methods using the following: vcftools, bcftools, vcfR, java, and perl. Any help would be greatly appreciated! Thank you.

gene vcf genome sequence • 195 views
ADD COMMENT
1
Entering edit mode

bcftools should do this, you can select all hom-ref/het/hom-alt loci in a subset of samples. You might need to run the query a few times, but it should be straightforward.

ADD REPLY

Login before adding your answer.

Traffic: 1124 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6