3.2 years ago by
While qctool will convert to VCF format without a sample file, this is only useful if you do not need to know the sample IDs, as when one does this, it generates dummy IDs in the VCF like this:
sample_1 sample_2 sample_3 sample_4 ...
In all the work we do, we need to know which sample is which, so we have to keep track of sample IDs and can't use dummy sample IDs.
If you do have a sample file in addition to your gen file, then Mega2 can convert from IMPUTE2 format to VCF format. See the Mega2 documentation for details.