Hello everyone! I need a hand to understand how to perform an imputation performance comparison. I performed an imputation on Michigan Imputation Server using these settings:
- Reference Panel: HRC r1.1 2016
- Phasing: Eagle v2.4
- Population (for QC only): Other/mixed
- Mode: quality control & imputation
- No rsq filter
- imputation is run with Minimac4
I have to perform a comparison between hard-calls variants (SNPs not included in the imputation which passed a QC) and the the hard-calls extracted from the dosages file from HRC imputation, using the GATK tool genotype concordance. Someone can explain how to proceed or can give me some advise and where to search? On the webpage of GATK there are not so clear information.
Many thanks in advance.