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?
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Justin
See this link:
In short, the MAQ paper is where the method is described:
Thanks!
For those interested in the math, see the heading "Consensus genotype calling" in the "Methods" section of the paper.
Basically, it's a Bayesian probability model where you want P(genotype g | observed data D), which you can get from Bayes' theorem if you have P(D | g), which the paper explains how to get. Then you estimate g as g* = argmax[g] P(g | D)
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