A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data.

ABSTRACT: The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the pres

SUBMITTER: Andrews KR 

PROVIDER: S-EPMC6207459 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature