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phasing VCF files with missing genotype

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

phasing
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updated by bouchenak.chuxi • bouchenak.chuxi • written by summerday1112 • summerday1112

1 answer

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

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written by bouchenak.chuxi • bouchenak.chuxi

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