Question: Convert IMPUTE2 to VCF while keeping phase information
3
gravatar for lkmklsmn
3.1 years ago by
lkmklsmn860
United States
lkmklsmn860 wrote:

Hi,  

I have imputed genotypes using the IMPUTE2 software. Now I need to convert my IMPUTE2 formatted genotypes into VCF. I have used the qctool to do so. However, the resulting VCF file has lost the phasing information. Is there any tool that allows me to convert IMPUTE2 to VCF while keeping the phasing information?  

Thanks

conversion phasing impute2 vcf • 1.6k views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 3.1 years ago by lkmklsmn860
6
gravatar for lkmklsmn
3.1 years ago by
lkmklsmn860
United States
lkmklsmn860 wrote:

I ended up using shapeit (version v2.837) -convert function to convert IMPUTE2 to VCF while keeping phase information.

ADD COMMENTlink written 3.1 years ago by lkmklsmn860
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