Transferring Phase information from one VCF to another

Question

[ma17]

Hi,

I have two different VCFs, one with statistically phased data and the other with experimentally phased data. They have the same exact variants and samples.

The statistically phased VCF has no missing data and all variants are phased, while the experimentally phased data has some missing data, and some variants are unphased.

For sites that are missing or unphased in the experimentally phased data, I am trying to transfer the genotype and phase information from the statistically phased VCF. Is there a way to do this?

Thanks

Answer 1

[WouterDeCoster]

Have a look at WhatsHap!