Minimac4 Reference panel

Hello:

Is there any reason that All SNPs in the reference panel samples need to have genotype information. if there is one SNP in the ref VCF file, the M3VCFtools will not covert the VCF to M3VCF. But impute2 can perform imputation if the some variants in ref panel have missing genotypes.

Another question, the output of minimac4 is always phased vcf (even without phased information in reference panel). So is there any way to perform the genotype imputation instead of haplotypes? Thanks

Jul 11 '19 16:07 xtmgah

I believe that the Minimac3 file format will allow for missing date and Minimac4 should support the older format. You can use Minimac3 --processReference to convert your vcf file. I'm about 75% confident that this will work.

To the best of my knowledge, Minimac4 only supports haplotype imputation. If either your reference panel or your target is not phased, then the imputation accuracy will suffer.

Jul 12 '19 14:07 jonathonl

Thanks for your comment.

Jul 16 '19 13:07 xtmgah