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F1000Res. 2017 Oct 3;6:1795. doi: 10.12688/f1000research.12516.1. eCollection 2017.

Tools for annotation and comparison of structural variation.

Author information

1
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
2
Worcester Polytechnic Institute, Worcester, MA, USA.
3
Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA.
4
University of California, Berkeley, Berkeley, CA, USA.
5
Virginia Commonwealth University, Richmond, VA, USA.
6
Genome-scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD, USA.

Abstract

The impact of structural variants (SVs) on a variety of organisms and diseases like cancer has become increasingly evident. Methods for SV detection when studying genomic differences across cells, individuals or populations are being actively developed. Currently, just a few methods are available to compare different SVs callsets, and no specialized methods are available to annotate SVs that account for the unique characteristics of these variant types. Here, we introduce SURVIVOR_ant, a tool that compares types and breakpoints for candidate SVs from different callsets and enables fast comparison of SVs to genomic features such as genes and repetitive regions, as well as to previously established SV datasets such as from the 1000 Genomes Project. As proof of concept we compared 16 SV callsets generated by different SV calling methods on a single genome, the Genome in a Bottle sample HG002 (Ashkenazi son), and annotated the SVs with gene annotations, 1000 Genomes Project SV calls, and four different types of repetitive regions. Computation time to annotate 134,528 SVs with 33,954 of annotations was 22 seconds on a laptop.

KEYWORDS:

NGS; annotation; bioinformatics; structural variants; whole genome sequencing

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