Converting single nucleotide variants between genome builds: from cautionary tale to solution.

ABSTRACT: Next-generation sequencing studies are dependent on a high-quality reference genome for single nucleotide variant (SNV) calling. Although the two most recent builds of the human genome are widely used, position information is typically not directly comparable between them. Re-alignment gives the most accurate position information, but this procedure is often computationally expensive, and therefore, tools such as liftOver and CrossMap are used to convert data from one build to another. However, the positions of converted SNVs do not always match SNVs derived from aligned data, and in some instances, SNVs are known to change chromosome when converted. This is a significant problem when compiling sequencing resources or comparing results across studies. Here, we describe a novel algorithm to

SUBMITTER: Ormond C 

PROVIDER: S-EPMC8425424 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature