Commit 3ee54932 authored by Moustakas's avatar Moustakas
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Add ShivaSvCalling documentation

parent 6b106b2f
......@@ -186,6 +186,33 @@ To run the pipeline:
biopet pipeline shivavariantcalling -config MySettings.yml -run
### Only Structural Variant calling
It is possible to run Shiva while only performing the Structural Variant calling steps starting from BAM files. For this, there is a separate pipeline named `ShivaSvCalling`.
The difference from running Shiva, is that it will not convert the BAM files into fastq files first and it will omit any pre-processing or alignment steps.
It will call SVs based on the input alignment (BAM) files.
To view the help menu, type:
biopet pipeline ShivaSvCalling -h
Arguments for ShivaSvCalling:
-BAM,--inputbamsarg <inputbamsarg> Bam files (should be deduped bams)
-sample,--sampleid <sampleid> Sample ID
-library,--libid <libid> Library ID
-config,--config_file <config_file> JSON / YAML config file(s)
-cv,--config_value <config_value> Config values, value should be formatted like 'key=value' or
-DSC,--disablescatter Disable all scatters
To run `ShivaSvCalling`, the user needs to supply the input BAM files from the command line using the `-BAM` flag. It is not possible to provide them in a sample sheet as a config file.
No sample ID or library information is necessary.
To run the pipeline, you can type something like:
biopet pipeline ShivaSvCalling -BAM sampleA.bam -BAM sampleB.bam -config MySettings.yml -run
### Exome variant calling
If one calls variants with Shiva on exome samples and an ```amplicon_bed``` file is available, the user is able to add this file to the config file.
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