DOI: 10.1101/460345Nov 4, 2018Paper

Accurate sequence variant genotyping in cattle using variation-aware genome graphs

BioRxiv : the Preprint Server for Biology
Danang CrysnantoHubert Pausch

Abstract

Background: The genotyping of sequence variants typically involves as a first step the alignment of sequencing reads to a linear reference genome. Because a linear reference genome represents only a small fraction of sequence variation within a species, reference allele bias may occur at highly polymorphic or diverged regions of the genome. Graph-based methods facilitate to compare sequencing reads to a variation-aware genome graph that incorporates non-redundant DNA sequences that segregate within a species. We compared accuracy and sensitivity of graph-based sequence variant genotyping using the Graphtyper software to two widely used methods, i.e., GATK and SAMtools , that rely on linear reference genomes using whole-genomes sequencing data of 49 Original Braunvieh cattle. Results: We discovered 21,140,196, 20,262,913 and 20,668,459 polymorphic sites using GATK , Graphtyper , and SAMtools , respectively. Comparisons between sequence variant and microarray-derived genotypes showed that Graphtyper outperformed both GATK and SAMtools in terms of genotype concordance, non-reference sensitivity, and non-reference discrepancy. The sequence variant genotypes that were obtained using Graphtyper had the lowest number of mendelian inco...Continue Reading

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