Edinburgh Research Explorer

AlphaFamImpute: high accuracy imputation in full-sib families from genotype-by-sequencing data

Research output: Contribution to journalArticle

Related Edinburgh Organisations

Open Access permissions

Open

Documents

  • Download as Adobe PDF

    Rights statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

    Final published version, 240 KB, PDF document

    Licence: Creative Commons: Attribution (CC-BY)

Original languageEnglish
JournalBioinformatics
Early online date28 May 2020
DOIs
Publication statusE-pub ahead of print - 28 May 2020

Abstract

SUMMARY: AlphaFamImpute is an imputation package for calling, phasing, and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data is increasingly being used to genotype individuals, especially when SNP arrays do not exist for a population of interest. Low-coverage GBS produces data with a large number of missing or incorrect naïve genotype calls, which can be improved by identifying shared haplotype segments between full-sib individuals. Here we present AlphaFamImpute, an algorithm specifically designed to exploit the genetic structure of full-sib families. It performs imputation using a two-step approach. In the first step it phases and imputes parental genotypes based on the segregation states of their offspring (that is, which pair of parental haplotypes the offspring inherited). In the second step it phases and imputes the offspring genotypes by detecting which haplotype segments the offspring inherited from their parents. With a series of simulations we find that AlphaFamImpute obtains high accuracy genotypes, even when the parents are not genotyped and individuals are sequenced at less than 1x coverage.

AVAILABILITY AND IMPLEMENTATION: AlphaFamImpute is available as a Python package from the AlphaGenes website, http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute.

SUPPLEMENTARY INFORMATION: A complete description of the methods is available in the supplementary information.

Download statistics

No data available

ID: 149781530