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Hmm, I just got a very similar fatal error running MuTect2 from the GATK4-5 version. Tried using different Java versions and no difference. Also I noticed that the error is not consistently showing at the same place, sometimes it can run for 30 min,…
@shlee I can't find those input vcf files on the VerifyBamId website, can you link to them? If I am not mistaken some people are using HapMap for this purpose.
Hi @Geraldine_VdAuwera, Thanks for the clarification. You are right, it is important to distinguish between the different behaviours of different backends and/or use of docker. In my use case I am running everything on a backend similar to SGE (T…
Thanks for submitting the ticket. Hmm, I see your point regarding the versioning on login vs. compute nodes. For me this is trivial because I am using a shared filesystem so I guess I will just specify thebwa version in the input json.
Thanks @Ruchi, this was exactly what I needed! I actually had thought about using the runtime stanza but didn't have the courage because of: https://gatkforums.broadinstitute.org/wdl/discussion/6704/runtime and: https://github.com/broadinstitute…
Hah, fell into the same mistake. Although Pair indexing is described in one line here: https://software.broadinstitute.org/wdl/documentation/spec#pair-indexing It should probably also be in the zip command snippet itself. BTW this is a really …