How to merge different strain SNP vcf files into one combined vcf file with strain specificity.

Question

[AlicePsyche]

Hi,

I want to do allele specific binding analysis using ChIP-seq data but I have some problems with the first step: individualized genome construction.

In mouse, I found the vcf file with strain specificity like this format:

CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  129P2   129S1   129S5   AKR     A_J     BALB    C3H     C57BL   CAST    CBA

Each strain have one annotation column but I failed to find this vcf file of zebrafish(danRer7). I only got three separate SNP vcf files each regarding one specific strain(AB_strain.vcf, Tu_strain.vcf, WIK_strain.vcf). I am wondering if I could just combine them using bcftools(merge). I am not so familiar with the SNP data so any advice would be helpful.

Thanks in advance.

Answer 1

[Vivek]

You can merge them using GATK or VCF-merge from VCFtools as long as the strain names are specified as sample names within the VCF header. Be sure to specify the ploidy correctly if not diploid as most tools assume diploid by default.

[AlicePsyche]

Thanks for your help, now I have solved this problem using vcftools :)