GenomeWarp: an alignment-based variant coordinate transformation

Abstract Summary Reference genomes are refined to reflect error corrections and other improvements. While this process improves novel data generation and analysis, incorporating data analyzed on an older reference genome assembly requires transforming the coordinates and representations of the data...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics 2019-11, Vol.35 (21), p.4389-4391
Main Authors: McLean, Cory Y, Hwang, Yeongwoo, Poplin, Ryan, DePristo, Mark A
Format: Article
Language:English
Subjects:
Applications Notes
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Abstract Summary Reference genomes are refined to reflect error corrections and other improvements. While this process improves novel data generation and analysis, incorporating data analyzed on an older reference genome assembly requires transforming the coordinates and representations of the data to the new assembly. Multiple tools exist to perform this transformation for coordinate-only data types, but none supports accurate transformation of genome-wide short variation. Here we present GenomeWarp, a tool for efficiently transforming variants between genome assemblies. GenomeWarp transforms regions and short variants in a conservative manner to minimize false positive and negative variants in the target genome, and converts over 99% of regions and short variants from a representative human genome. Availability and implementation GenomeWarp is written in Java. All source code and the user manual are freely available at https://github.com/verilylifesciences/genomewarp. Supplementary information Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btz218