The output file

[JielinLi]

Hi,

I want to ask if the output file only contain GT without GP ?

Thank you!

[cnettel]

I'm sorry for not answering earlier. Yes, as the code is currently written. However, in main.cpp you can see that it actually finds the maximum genotype by reading the stats data structure and finding the maximum. It would be a rather small change to allow GP output instead by "just" emitting those values. We did so internally for other uses, but never directly to VCF.