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2015 ; 11
(12
): e1004572
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Wham: Identifying Structural Variants of Biological Consequence
#MMPMID26625158
Kronenberg ZN
; Osborne EJ
; Cone KR
; Kennedy BJ
; Domyan ET
; Shapiro MD
; Elde NC
; Yandell M
PLoS Comput Biol
2015[Dec]; 11
(12
): e1004572
PMID26625158
show ga
Existing methods for identifying structural variants (SVs) from short read
datasets are inaccurate. This complicates disease-gene identification and efforts
to understand the consequences of genetic variation. In response, we have created
Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework
for both structural variant calling and association testing, thereby bypassing
many of the difficulties that currently frustrate attempts to employ SVs in
association testing. Here we describe Wham, benchmark it against three other
widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate
Wham's ability to identify and associate SVs with phenotypes using data from
humans, domestic pigeons, and vaccinia virus. Wham and all associated software
are covered under the MIT License and can be freely downloaded from github
(https://github.com/zeeev/wham), with documentation on a wiki
(http://zeeev.github.io/wham/). For community support please post questions to
https://www.biostars.org/.
free
free
free
