Is there a tutorial available for calling CNVs in germline DNA with GATK4? I see an earlier post for somatic CNVs but could not locate one for germline CNVs.
Not yet. I think there are plans to have one in the near future (probably after the GATK4 release).
Any news on that?
Or at least a short HOWTO on how to call CNVs in germline DNA? This is not very obvious ...
ok, I found https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_copynumber_GermlineCNVCaller.php ...
There are plans to have a tutorial on this, but I need to check in with the developer on where it stands. It is coming soon..