MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

For complete details, please see the publication in Nature Biotechnology:

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnology (2013).doi:10.1038/nbt.2514

Download after login.

http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/...

Note that muTect-1.1.4-bin.zip is a zipbomb. Useless developers.


cd /usr/local/src/MUTETC
mkdir /usr/local/src/1.1.4
mv muTect-1.1.4-bin.zip 1.1.4
unzip muTect-1.1.4-bin.zip
mkdir -p /usr/local/mutect/1.1.4
cd /usr/local/mutect/1.1.4
cp /usr/local/src/MUTECT/1.1.4/* .


Change to the appropriate modules directory, check for .desc and .version and .base, create a symblink to .base


cd /usr/local/Modules/modulefiles/mutect
ln -s .base 1.1.4


The .base module takes the following form.


#%Module1.0#####################################################################
##
## $name modulefile
##
set ver [lrange [split [ module-info name ] / ] 1 1 ]
set name [lrange [split [ module-info name ] / ] 0 0 ]
set loading [module-info mode load]
set desc [join [read [ open "/usr/local/Modules/modulefiles/$name/.desc" ] ] ]
set subver [lrange [split $ver - ] 0 0 ]
set compiler [lrange [split $ver - ] 2 2 ]
proc ModulesHelp { } {
puts stderr "\tThis module sets the envinronment for $name v$ver"
}
module-whatis "$desc (v$ver)"
if { $loading && ![ is-loaded java ] } {
module load java
}
prepend-path PATH /usr/local/$name/$ver