Computational Haplotype Inference from Pooled Samples.

Computationally inferring the identities and their relative frequencies from pooled samples that are whole-genome or segmentally genotyped or sequenced (e.g., using next-generation sequencing) in a pool is useful for population genetics analysis. To carry out such analysis, one needs to understand basics of how to use high-performance computing (HPC) facilities and the specifics of corresponding computational tools. Here, we describe the basic knowledge and step-by-step usage of a number of tools for haplotype inference on genotyping or next-generation sequencing data.