I have a VCF file and many lines have multiple ALT alleles such as:
1 104159 . CA C,TA,TTT
I have an algorithm that takes genotype data in a 0,1,2 matrix form. I am wondering if there are any standards or best practices in how to turn VCF lines with multiple ALT alleles (0/0,0/1,0/2,1/2,2/3) into 0,1,2 genotype form.