Performance comparison of SNP detection tools with illumina exome sequencing data--an assessment using both family pedigree information and sample-matched SNP array data.

ABSTRACT: To apply exome-seq-derived variants in the clinical setting, there is an urgent need to identify the best variant caller(s) from a large collection of available options. We have used an Illumina exome-seq dataset as a benchmark, with two validation scenarios--family pedigree information and SNP array data for the same samples, permitting global high-throughput cross-validation, to evaluate the quality of SNP calls derived from several popular variant discovery tools from both the open-source and commercial communities using a set of designated quality metrics. To the best of our knowledge, this is the first large-scale performance comparison of exome-seq variant discovery tools using high-throughput validation with both Mendelian inheritance checking and SNP array data, which allows us to

SUBMITTER: Yi M 

PROVIDER: S-EPMC4081058 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature