I have a vcf file that consist multi allelic and I need to do a snpmatrix to do a machine learning later
So, for example if I have a genotype like : 0/0 , 1/1 , 0/2 , 1/2 , 0/1, 2/2
how can I do a snpmatrix ?
0/0 < for example 0 because it homo ref
0/1 and 0/2 < 1 because it hetero
1/1 and 2/2 < 2 because it homo alt
I have some genotype as missing like ./1 or ./. so what the suggestion for missing genotype?