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)
-cv,--config_value <config_value> Config values, value should be formatted like 'key=value' or
'namespace:namespace:key=value'
-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.