Background

GASV was identified following reading of this literature review for use in detecting structural variants from mapped reads in bam files. The choice was somewhat arbitrary, although GASV appears to be a good option as it combines read depth and discordant mapping information to detect structural variants.

Installing GASV

GASV is available on Google Drive. To install, simply untar the downloadable archive and place in $PATH or a directory that is already in $PATH. The software requires Java to run. Installation commands:

sudo su
cd /usr/local/src
mv /path/to/GASVrelease.tar.gz /tmp/
tar xvzf /tmp/GASVrelease.tar.gz
cd gasv
./install
ln -s bin/* /usr/local/bin

Running GASV

Instructions for running GASV can be found in a pdf file in the Google Drive page. The following sections are mostly repetitions of what is in this document.

Convert bam to GASV

From our previous dataset generated on Pawsey (see Running multiple genome analysis), we use the bam files as input. These bam files have been quality filtered and made to conform to all GATK standards. Before running GASV, files must be converted to a suitable input fromat from the original bams.