I am using VcfTools to parser VCF files.
I can use it to generate a 012 matrix. This matrix is 2D, with the shape of (num of individuals, num of SNPs).
In each cell in the matrix, there is the number of occurrences, of the alternative allele for the specific SNP in a specific individual.
This is great for a biallelic data - means for every SNP there is a single allele.
In my case there are at most
n alleles per SNP,and I would like to have
n matrices, each one is for an "allele index" and it specify in each cell how many occurrences of that allele are, in the specific Individual in the specific SNP.
Does anyone familiar with a tool that can provide that?