Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.

ABSTRACT:

Background

High-throughput sequencing is rapidly becoming common practice in clinical diagnosis and cancer research. Many algorithms have been developed for somatic single nucleotide variant (SNV) detection in matched tumor-normal DNA sequencing. Although numerous studies have compared the performance of various algorithms on exome data, there has not yet been a systematic evaluation using PCR-enriched amplicon data with a range of variant allele fractions. The recently developed gold standard variant set for the reference individual NA12878 by the NIST-led "Genome in a Bottle" Consortium (NIST-GIAB) provides a good resource to evaluate admixtures with various SNV fractions.

Results

Using the NIST-GIAB gold standard, we compared the performance of five popular somatic SNV ca

SUBMITTER: Xu H 

PROVIDER: S-EPMC3986649 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature