Determine zygosity from FASTA files

[ashkot]

Hi all,
I am working with full chromosome FASTA file and am looking at specific sequences.

I wanted to know if there is a way to determine if the person homozygous or hetrozygous. Specifically I am looking at SNP sequences so I know the wildtype and risk allele beforehand.

Any help in this area would be highly appreciated.

Thanks,
Ashwin

[swbarnes2]

In theory, your fasta might have an ambiguous letter if the sample has both alleles of a simple SNP. For instance, if your SNP is an A/G SNP, and your sample possesses both alleles, there might be an R at that locus. But that depends on how your fasta was constructed, and I'm not sure at all that that kind of information is usually expressed in a FASTA sequence.