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.