I have a vcf of mitochondrial chromosome. I am interested to generate a sequence (fasta like ) for the variant positions. It has been pretty straight forward for positions with homoplasmic (GT 0/0) Ref or homoplasmic Alt ( GT 1/1) to pick Ref and Alt respectively. However, there are several heteroplasmic positions ( GT 0/1) where allelic read depths of Ref and Alt are almost the same. Which alleles should I consider (Ref or Alt) in such cases?
Dinesh Velayutham
Jigme Dorji This depends primarily on your further application.
You can use the major allele (defined by the population)
Or if you want to study the variant's impact, you should use the alt allele. Typically concensus sequences generated by samtools using VCF files adapt this approach.
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