Pre-imputation checks using 1000G data (hg19) for a hg38 VCF

Question

[guoweidora]

I'm trying to use the pre-imputation checks here https://www.well.ox.ac.uk/~wrayner/tools/ to check a vcf (on the hg38 assembly) on the 1000G phase 3 v5 data, which is hg19, before imputing using the MIS.

I am trying to use 1000G phase3 V5 reference to impute my hg38 genotype data. I am trying to run

perl HRC-1000G-check-bim.pl \ -b chr1.bim \ -f chr1.freq.frq \ -r 1000GP_Phase3_combined.legend \ -g -p EUR \

Which is not working since mismatch between input and ref version.

May I know if I need to liftover my data to hg19 for purpose of doing imputation in Michigan imputation server.

Please help. thanks.

[bk11]

Basically, you necessarily do not have to liftover your data to hg19 from hg38. You can do pre-imputation QC using TOPMed reference data instead which in hg38.