Choice of transcripts and software has a large effect on variant annotation.

ABSTRACT:

Background

Variant annotation is a crucial step in the analysis of genome sequencing data. Functional annotation results can have a strong influence on the ultimate conclusions of disease studies. Incorrect or incomplete annotations can cause researchers both to overlook potentially disease-relevant DNA variants and to dilute interesting variants in a pool of false positives. Researchers are aware of these issues in general, but the extent of the dependency of final results on the choice of transcripts and software used for annotation has not been quantified in detail.

Methods

This paper quantifies the extent of differences in annotation of 80 million variants from a whole-genome sequencing study. We compare results using the RefSeq and Ensembl transcript sets as the basis f

SUBMITTER: McCarthy DJ 

PROVIDER: S-EPMC4062061 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature