Does either the mother or father's chromosome always come first in the comma separated ALT of a VCF?
Or is it impossible to tell which chromosome/ ploid came from which parent?
ALT = [A, T]
Are the slash separated "0/0" and "1" in any way indicative of the actual chromosome that the variant falls under?
I guess if ploids are split and read one at a time... the first position would at least always correspond to the same sequence for the length of the read?
But how can you trust a codon type when you don't know what sample comes from what index order in the alt column? https://en.wikipedia.org/wiki/DNA_codon_table