Problem with binomial calculation

[chundruv]

Hi Petr,

I noticed that when calculating the binomial of allele depth there is an issue when there is a multiallelic variant, which is not a problem when normalising first.

I had one position which was set to missing with the setGT when done before splitting, and not after splitting. It was a 0/6 genotype, the LAD was 19,21, and the GQ was 15. When you print out the binom before splitting it is giving a “.”, whereas after splitting it is giving the actual probabilities. However, when I manually change it to 0/1, it gives the correct probability without splitting so it’s a problem with the non-0/1 genotypes, it doesn’t like that.

Also, is there an option when splitting multiallelics to set the non-ref calls on other alleles to missing? Just thinking that if you set it to homref it might not be the best for some analyses. Also, is there a way to update the DP and other format fields when splitting?

Thanks, Karitk