From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software.

ABSTRACT: Scientists working with single-nucleotide variants (SNVs), inferred by next-generation sequencing software, often need further information regarding true variants, artifacts and sequence coverage gaps. In clinical diagnostics, e.g. SNVs must usually be validated by visual inspection or several independent SNV-callers. We here demonstrate that 0.5-60% of relevant SNVs might not be detected due to coverage gaps, or might be misidentified. Even low error rates can overwhelm the true biological signal, especially in clinical diagnostics, in research comparing healthy with affected cells, in archaeogenetic dating or in forensics. For these reasons, we have developed a package called pibase, which is applicable to diploid and haploid genome, exome or targeted enrichment data. pibase extracts det

SUBMITTER: Forster M 

PROVIDER: S-EPMC3592472 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature