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F1000Res. 2017 Apr 7;6:443. doi: 10.12688/f1000research.11254.1. eCollection 2017.

DangerTrack: A scoring system to detect difficult-to-assess regions.

Author information

1
New York University School of Medicine, New York, NY, 10016, USA.
2
Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21202, USA.
3
National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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Contributed equally

Abstract

Over recent years, multiple groups have shown that a large number of structural variants, repeats, or problems with the underlying genome assembly have dramatic effects on the mapping, calling, and overall reliability of single nucleotide polymorphism calls. This project endeavored to develop an easy-to-use track for looking at structural variant and repeat regions. This track, DangerTrack, can be displayed alongside the existing Genome Reference Consortium assembly tracks to warn clinicians and biologists when variants of interest may be incorrectly called, of dubious quality, or on an insertion or copy number expansion. While mapping and variant calling can be automated, it is our opinion that when these regions are of interest to a particular clinical or research group, they warrant a careful examination, potentially involving localized reassembly. DangerTrack is available at https://github.com/DCGenomics/DangerTrack.

KEYWORDS:

Breakpoint; CNV; Clinical Genetics; SNP; Structural Variants

Conflict of interest statement

Competing interests: No competing interests were disclosed.

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