- A dry run can be performed to see if the scheduling and creating of the pipelines jobs performs well. Nothing will be executed only the job commands are created. If this succeeds it's a good indication you actual run will be successful as well.
- Each pipeline can be found as an options inside the jar file Biopet[version].jar which is located in the target directory and can be started with `java -jar <pipelineJarFile>`
~~~
java -jar Biopet(version).jar (pipeline of interest) (pipeline options)
~~~
### Shark Compute Cluster specific
In the SHARK compute cluster, a module is available to load the necessary dependencies.
...
...
@@ -104,8 +116,6 @@ There are multiple configs that can be passed to a pipeline, for example the sam
- VcfToTsv
- WipeReads
## Developers
### Compiling Biopet
...
...
@@ -117,10 +127,9 @@ There are multiple configs that can be passed to a pipeline, for example the sam
5. run `mvn verify` to compile and package or do `mvn install` to install the jars also in local maven repository
The GATK-pipeline is build for variant calling on NGS data (preferably Illumina data).
It uses the <ahref="https://www.broadinstitute.org/gatk/guide/best-practices"target="_blank">best practices</a>) of GATK in terms of there approach to variant calling.
It is based on the <ahref="https://www.broadinstitute.org/gatk/guide/best-practices"target="_blank">best practices</a>) of GATK in terms of there approach to variant calling.
The pipeline accepts ```.fastq & .bam``` files as input.