snpmatix for multi allelic

Question

[arwa.ahmad95]

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 ?

I think

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

1/2 ???

any suggestion?

also,

I have some genotype as missing like ./1 or ./. so what the suggestion for missing genotype?