Annotate VCF to include dosage

Question

[Nicholas Mancuso]

Is there an easy way to annotate a VCF to include dosages? I have a VCF with phred-scaled likelihoods (PL), but no dosages (DS).

I know that there is a bcftools plugin to compute dosages based off of the PL tag, but it isn't clear how to incorporate these output into the original VCF w/o having to write my own custom scripts.

Is the bcftools annotate able to handle the output from the plugin or is there another way to annotate variant calls with the DS info?

Answer 1

[Nicholas Mancuso]

I ended up writing my own c++ program to do this quickly as possible. It is fairly bare-bones, but shouldn't be too hard to extend it to properly take care of other user's edge cases.

https://github.com/quattro/DS2VCF