I have a consensus fasta file generated by samtools/bcftools/vcfutils as discussed in a previous post here: How to generate a consensus fasta sequence from SAM tools pileup?
In some sites, I see e.g. R, which means that site was heterozygous A/G.
How does it determine it's heterozygous? E.g. if you see 50 A's and 39 G's, how do you know it's a het? By using a minor allele % threshold? Or using a probability model? If it uses probability, are there any references out there that describe the math?