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. Obviously, very few of the variants in the vcf are matching locations in the hg19 1000G data.
My question is, is there a version of the pre-imputation checks that works on a hg38 dataset, or is it possible to use a lifted version of the hg19 data for these checks?
I've tried GATK LiftoverVcf to convert my hg38 data back to hg19, but as the vcf contains indels, I'm getting a lot of rejected variants because of the differences in assemblies.
Since your data is in hg38 build, you can perform pre-imputation checks following the section in Usage with the TOPMed reference panel in https://www.well.ox.ac.uk/~wrayner/tools/. You do not have to perform liftover for these checks.
That seems to have sorted it. I was following an older protocol which used hg19 vcfs & the hg19 reference 1000G panel, so I'm going to update it.
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