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