My first walker for the GATK : my notebook

This is my first notebook for developping a new Walker for the Genome Analysis Toolkit. This post was mostly inspired by the following pdf: kvg_20_line_lifesavers_mad_v2.pptx.pdf.

Get the sources

git clone http://github.com/broadgsa/gatk.git GATK.dev

the javac compiler also requires the following library from google :http://code.google.com/p/cofoja/.

A first "Short-Reads" walker

The following class ReadWalker scans the reads and print them as fasta. The @Output annotation tells the GATK that we're going to channel our output through the java.io.PrintStream object. This field is automatically filled by the application runtime.

Compilation

javac -cp /path/to/GenomeAnalysisTK.jar:/path/to/cofoja-1.0-r139.jar:. \
 -sourcepath src \
 -d tmp src/mygatk/HelloRead.java
jar cvf HelloRead.jar -C tmp .

Running

Here I'm using a BAM from the 'examples' folder of samtools. (We need to pre-process this BAM with picard AddOrReplaceReadGroups). We then use our library as follow:

java -cp path/to/GenomeAnalysisTK.jar:HelloRead.jar \
org.broadinstitute.sting.gatk.CommandLineGATK -T HelloRead \
 -I test.bam \
 -R ${SAMTOOLS}/examples/ex1.fa 

Result:

The Makefile

That's it, Pierre