BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity.

ABSTRACT:

Background

Accurate genomic variant detection is an essential step in gleaning medically useful information from genome data. However, low concordance among variant-calling methods reduces confidence in the clinical validity of whole genome and exome sequence data, and confounds downstream analysis for applications in genome medicine.Here we describe BAYSIC (BAYeSian Integrated Caller), which combines SNP variant calls produced by different methods (e.g. GATK, FreeBayes, Atlas, SamTools, etc.) into a more accurate set of variant calls. BAYSIC differs from majority voting, consensus or other ad hoc intersection-based schemes for combining sets of genome variant calls. Unlike other classification methods, the underlying BAYSIC model does not require training using a "gold standard" o

SUBMITTER: Cantarel BL 

PROVIDER: S-EPMC3999887 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature