phasing VCF files with missing genotype

Question

[summerday1112]

I want to phasing a VCF file with missing value(./.), the output I want get (a VCF also)is all the genotype are phased, but the ./. will not be imputed.

I have tried shapeit and beagle, but both of them impute the missing genotype(./.). does anyone know how to avoid impute missing value(./.) when phasing

Answer 1

[bouchenak.chuxi]

Hello ,

i think you can check EagleImp-Web, according to the article it has the possibility to check or not ''the imputation" step when phasing.

PS: for now it only works with human data