Updates to the human hg38 analysis pipeline

At Gencove, we make an effort to keep current on the most up-to-date developments in the refinement and enhancement of existing imputation reference panels and genomic datasets. To this end, we have released an imputation pipeline for humans based on a liftover from the original 1000 Genomes Phase 3 release to the most recent build of the human reference genome (GRCh38); this is now accessible as a publicly available pipeline configuration.

Although we recently released a beta version of the 1000 Genomes reference panel based on a resequencing effort by the New York Genome Center, it is less well-validated and as such we currently recommend using this liftover release for production purposes instead. Preliminary testing shows that the lifted-over panel provides a ~2.5% increase in genotype concordance to truth data for an imputed European-ancestry individual relative to the ‘natively-called’ panel.