svParser for SV

svParser ^[1] is a tool to filter, genotype, annotate and combine VCF files from structural variant callers LUMPY, DELLY and novobreak.

Installation

git clone https://github.com/nriddiford/svParser.git
wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib
eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`

Add the following lines to your bash_profile (or .profile/.bashrc/):

eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`
export MANPATH=$HOME/perl5/man:$MANPATH

Summarize variants

perl script/svParse.pl -v data/Droso_R7.lumpy.vcf -m l

Important: Variants called by LUMPY must also be genotyped by SVTyper

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1. https://github.com/bardin-lab/svParser ↩︎