created by LeeTL1220
on 2016-04-06
The WDL for GATK CNV is currently under development.
WDL for the GATK CNV/ACNV workflow can be found in the gatk-protected repo:
https://github.com/broadinstitute/gatk-protected/tree/master/scripts/wdl
Updated on 2016-05-20
From micknudsen on 2016-06-01
How do you access the tools required for CNV analysis? I have installed GATK 4 Alpha, but when I run “./gatk-launch —list”, the only CNV tool available is CalculateTargetCoverage.
From LeeTL1220 on 2016-06-01
@micknudsen You are running the gatk (public) jar file. You need the gatk-protected jar file. You can download a pre-built one below.
Jar file: http://www.broadinstitute.org/~lichtens/gatk4cnv/gatk-protected.jar
Or go to the repo: https://github.com/broadinstitute/gatk-protected
From micknudsen on 2016-06-01
>
LeeTL1220 said: >
micknudsen You are running the gatk (public) jar file. You need the gatk-protected jar file. You can download a pre-built one below.
> Jar file: http://www.broadinstitute.org/~lichtens/gatk4cnv/gatk-protected.jar
> Or go to the repo: https://github.com/broadinstitute/gatk-protected
Thanks!
From Geraldine_VdAuwera on 2016-07-26
FYI from here on out you can get the latest version of the GATK4 jar here: https://software.broadinstitute.org/gatk/download/alpha