Conversion of IMPUTE2 .gen format to .vcf format with dosage value (DS)

[kumardeep chaudhary]

Hi,

I have .gen file with 3 genotype probability values for each sample. I need to convert to .vcf file where I get DS flag and corresponding dosage value for each sample.

How can I achieve this using mega2.

PS: I used qctool earlier but in the output vcf I have GP flag with 3 values for each sample.

Thanks.

Kumar

[Dan Weeks]

Dear Kumar,

Mega2 does not currently support conversion of 3 genotype probability values to a DS dosage value.

I think the DosageConverter software available here https://genome.sph.umich.edu/wiki/DosageConvertor will probably do what you want if you run it with the

--tag GP

option.

Hope that helps,

Dan Weeks