RIG: Recalibration and interrelation of genomic sequence data with the GATK.

ABSTRACT: Recent advances in variant calling made available in the Genome Analysis Toolkit (GATK) enable the use of validated single-nucleotide polymorphisms and indels to improve variant calling. However, large collections of variants for this purpose often are unavailable to research communities. We introduce a workflow to generate reliable collections of single-nucleotide polymorphisms and indels by leveraging available genomic resources to inform variant calling using the GATK. The workflow is demonstrated for the crop plant Sorghum bicolor by (i) generating an initial set of variants using reduced representation sequence data from an experimental cross and association panels, (ii) using the initial variants to inform variant calling from whole-genome sequence data of resequenced individuals, an

SUBMITTER: McCormick RF 

PROVIDER: S-EPMC4390580 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature