I am analying a data set for a user interested in looking at variants in the MHC gene of coyotes. I have used Freebayes to generate a VCF file. The user would now like haploytypes, does anyone know how to decipher that info from a file such as this vcf:
Hi again everyone,
Ram has asked that I provide more clarity on the purpose of of my exercise. So here goes:
The user is looking at SNPs that are linked on a single functional gene in the coyote genome and would like to decipher haploytpes of these SNPs because different haploytypes are indicative of different levels of resistance to things such as Mange.
If there are 4 SNPs across the amplicon my user needs to know how these SNPs are inherited in an allele form, meaning which SNPs were on the same strand of DNA.