Abstract
SummaryAlphaFamImpute 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 are 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 (i.e. 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 <1x coverage.Availability and implementationAlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute.Supplementary information Supplementary data are available at Bioinformatics online.
Highlights
AlphaFamImpute is a software package for calling, phasing, and imputing genome-wide genotypes in full-sib families when individuals are genotyped with single nucleotide polymorphism (SNP) array or genotyping-by-sequencing (GBS) data
GBS is an alternative to SNP arrays (Baird et al, 2008; Davey et al, 2011; Elshire et al, 2011), where specific restriction enzymes are used to focus sequencing resources on a limited number of cut sites
GBS is attractive for species without an existing SNP array or as a low-cost alternative to SNP arrays (e.g., Gorjanc et al, 2015, 2017)
Summary
AlphaFamImpute is a software package for calling, phasing, and imputing genome-wide genotypes in full-sib families when individuals are genotyped with single nucleotide polymorphism (SNP) array or genotyping-by-sequencing (GBS) data. Some existing software packages can be used for genotype calling and imputation from GBS data, for example, Beagle (Browning and Browning, 2009), STITCH (Davies et al, 2016), AlphaPeel (Whalen et al, 2018) or magicimpute (Zheng et al, 2018). These software packages are not designed to exploit specific structure of haplotype sharing observed in large full-sib families. We describe our software package AlphaFamImpute that leverages this particular population structure to improve the accuracy of calling, phasing and imputing genome-wide genotypes and which decreases run-time compared to existing methods. We focus on outbred full-sib families because this represents a population structure commonly found in research populations, and in animal and plant breeding programs
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