Simulate genotype likelihoods
I am looking for a package to simulate genotype likelihoods using a vcf file. Something similar to ANGSD tool http://popgen.dk/angsd/index.php/MsToGlf But instead of msms input, I have simulated vcf files. I was thinking to simulate reads (using the vcf) and then call genotypes and GL. But maybe there is a workaround ?
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For which purpose do you wish to simulate these? I am not aware of any program that oes htis, but I can easily think of how it could be performed manually using, for example, AWK commands.