Dear All, I have a VCF files that contains SNPs belonging to 3-lines of chicken, wnere one VCF is unique to line A, other is unique to line B and the 3rd is a common SNPs in both A and B. I would like to get a picture of let say Chromosome 1 where mutations from the 3-files are colored and mapped on chromosome 1. I have been trying to use ChromMap, but I realized it needs to fill in txt files from the VCF file which is rather hard to do, as VCF files contains thousands of SNPs. Are any of you aware of a tool that could draw that for me, but using VCF file as input ?

Thanks