Originally posted by colindaven
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However, what I do is to run Dindel in pooled mode, and then use the "makeGenotypeLikelihoodFilePooled.py" script that comes with the program. This script prints a file with the likelihoods for homozygous ref/ref, heterozygous ref/alt and homozygous ref/ref - grabbing only the two homozygous likelihoods (ignoring the heterozygous likelihood) from this file allows me to force homozygosity (though then I have to compute some measure of confidence myself, e.g. a likelihood ratio or a posterior probability).
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