Detecting selected haplotype blocks in evolve and resequence experiments.

ABSTRACT: Shifting from the analysis of single nucleotide polymorphisms to the reconstruction of selected haplotypes greatly facilitates the interpretation of evolve and resequence (E&R) experiments. Merging highly correlated hitchhiker SNPs into haplotype blocks reduces thousands of candidates to few selected regions. Current methods of haplotype reconstruction from Pool-seq data need a variety of data-specific parameters that are typically defined ad hoc and require haplotype sequences for validation. Here, we introduce haplovalidate, a tool which detects selected haplotypes in Pool-seq time series data without the need for sequenced haplotypes. Haplovalidate makes data-driven choices of two key parameters for the clustering procedure, the minimum correlation between SNPs constituting a cluster an

SUBMITTER: Otte KA 

PROVIDER: S-EPMC7754423 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature