somatic-benchmark: An R repository from lbergelson

Tools for comparing somatic variant calling tools.

7/25/2013: This is a work in progress. Tools are incomplete, untested, undocumented, and subject to change.

This is the new home for the SomaticSpike walker.

INSTALLATION Assuming you have perl and python 2 installed already and are using bash as your shell. Also requires java 7.

To run with indelocator(assuming access to the broad network):

clone necessary repos

 git clone git@github.com:broadinstitute/somatic-benchmark
 git clone git@github.com:broadinstitute/indelocator
 git clone git@github.com:broadgsa/gatk-protected

build gatk-protected including SomaticSpike:

 cd gatk-protected
 ant -Dexternal.dir=../somatic-benchmark

build gatk-protected again with indelocator
```
 ant -Dexternal.dir=../indelocator
```
be sure that you built Queue
```
 ant queue
```
move to the somatic-benchmark directory
```
 cd ../somatic-benchmark
```
edit make_vcfs.pl and set GATK_BIN to your gatk jar file which is gatk-protected/dist/GenomeAnalysisTK.jar
edit tool-scripts/runIndelocator.sh
-set LIBDIR to point to your indelocator directory
-set GATKJAR to point to your gatk jar (or set the GATK environmental variable)
install this particular unstable build of oncotator
a. deactivate any existing python virtual environment (will do nothing if you don't have one active)
```
 deactivate
```
b. activate a new virtual environment for oncotator
```
 source /xchip/cga1/lichtens/test_oncotator/test_env/bin/activate  
 # it helps to add this to your .my.bashrc so you don't forget   
```
c. check that you have the right version
```
 which oncotator 
 #should display /xchip/cga1/lichtens/test_oncotator/test_env/bin/oncotator
```
(d. to return to your regular python environment later, use deactivate)

run GenerateBenchmark.scala

 java -jar gatk-protected/dist/Queue.jar -S GenerateBenchmark.scala -run -bsub

run RunBenchmark.scala with indelocator

java -jar gatk-protected/dist/Queue.jar -S RunBenchmark.scala -t Indelocator -run -bsub

analysis module is incomplete...

lbergelson/somatic-benchmark