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Structural Variation Discovery Pipeline
do you have any general guideline, also not official, about Structural Variation Discovery? I used only the tool reported above but I do not know if I have to use additional tools or how to filter my results by Quality values... or if there is a youtube tutorial, workshop slides?
I have as output the following files:
The file that I have to use as final output is "sample_inv_del_ins.vcf" ?
In the directory of GATK I found (local installation, linux server)
In the file "run_whole_pipeline.sh" I can see that I could use also the ExtractSVEvidenceSpark after StructuralVariationDiscoveryPipelineSpark tool ...
I have to work in case-mode or in cohort-mode (if available)
I appreciate also any help from the other users.