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The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle.

Audald Lloret-VillasHubert PauschAlexander S Leonard
Published in: Genetics, selection, evolution : GSE (2023)
Variant genotyping is more accurate with DeepVariant than GATK. DeepVariant is therefore suitable to establish bovine haplotype reference panels. Medium-sized breed-specific haplotype reference panels and large multibreed haplotype reference panels enable accurate imputation of low-pass sequencing data in a typical cattle breed.
Keyphrases
  • high resolution
  • single cell
  • high throughput
  • genome wide
  • electronic health record
  • machine learning