phase trios

Question

[alexmondaini]

Hi guys,

I have some vcf files from mother father and child and I need to phase the child vcf file using mother and father information. Any advice on recent software that can accomplish that task ? I was having a look at https://odelaneau.github.io/shapeit4/ but it seems to be a bit convoluted to install and I have not identified anything on the documentation that says that it can phase trios.

Thanks.

Answer 1

[4galaxy77]

Maybe try trioPhaser

[alexmondaini]

Yes, I'm trying this tool right now.It actually uses SHAPEIT4 in the background. I was wondering if BEAGLE or IMPUTE2 can do trio phasing, but it seems like it's only possible to make population based phasing.