Commit 55fc13c4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add documentation for ShivaVariantcalling

parent 36ddbb2a
......@@ -24,6 +24,10 @@ The pipeline accepts ```.fastq & .bam``` files as input.
Note that one should first create the appropriate [configs](../general/config.md).
### Full pipeline
The full pipeline can start from fastq or from bam file. This pipeline will include pre process steps for the bam files.
To get the help menu:
~~~
java -jar </path/to/biopet.jar> pipeline shiva -h
......@@ -37,11 +41,36 @@ Arguments for Shiva:
To run the pipeline:
~~~
java -jar </path/to/biopet.jar> pipeline shiva -run -config MySamples.json -config MySettings.json
java -jar </path/to/biopet.jar> pipeline shiva -config MySamples.json -config MySettings.json -run
~~~
To perform a dry run simply remove `-run` from the commandline call.
### Just variantcalling
This will not do any pre process steps on the bam files.
To get the help menu:
~~~
java -jar </path/to/biopet.jar> pipeline shivavariantcalling -h
Arguments for ShivaVariantcalling:
-BAM,--inputbams <inputbams> Bam files (should be deduped bams)
-sample,--sampleid <sampleid> Sample ID (only effects summary and not required)
-library,--libid <libid> Library ID (only effects summary and not required)
-config,--config_file <config_file> JSON config file(s)
-DSC,--disablescatter Disable all scatters
~~~
To run the pipeline:
~~~
java -jar </path/to/biopet.jar> pipeline shivavariantcalling -config MySettings.json -run
~~~
To perform a dry run simply remove `-run` from the commandline call.
----
## Variantcaller
......@@ -100,6 +129,7 @@ To view all possible config options please navigate to our Gitlab wiki page
}
}
},
"reference": "<location of fasta of reference>",
"variantcallers": [ "haplotypecaller", "unifiedgenotyper" ],
"output_dir": "<output directory>"
}
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment