CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.

ABSTRACT:

Background

Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical data. Provision of consistent, clinically applicable variant annotation of NGS data has proved difficult, particularly of indels, an important variant class in clinical genomics. Annotation in relation to a reference genome sequence, the DNA strand of coding transcripts and potential alternative variant representations has not been well addressed. Here we present tools that address these challenges to provide rapid, standardized, clinically appropriate annotation of NGS data in line with existing clinical standards.

Methods

We developed a clinical sequencing n

SUBMITTER: Munz M 

PROVIDER: S-EPMC4551696 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature