Evaluation of variant identification methods for whole genome sequencing data in dairy cattle.

ABSTRACT:

Background

Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less well documented. We explored the consequences of commonly recommended preparatory steps and the effects of single and multi sample variant identification methods using four publicly available software applications (Platypus, HaplotypeCaller, Samtools and UnifiedGenotyper) on whole genome sequence data of 65 key ancestors of Swiss dairy cattle populations. Accuracy of calling next-generation sequence variants was assessed by comparison to the same loci from medium and hi

SUBMITTER: Baes CF 

PROVIDER: S-EPMC4289218 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature