jar for mutect 1.1.7

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Knight Ni

• April 19, 2020 17:08

Dear GATK support,

 

I am trying to run pureCN for CNV with WES data.  pureCN requires mutect 1.1.7, but I am having trouble compiling it from source.  Could you provide pre-compiled mutect 1.1.7 jar file?  I have been googling around but can not find it anywhere.

 

Thank you so much.

 

Qi Zhang

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  Bhanu Gandham

  • April 22, 2020 14:57

  Here is a list of all the GATK releases: https://github.com/broadinstitute/gatk/releases

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  Raquel Manzano

  • August 19, 2020 10:21

  Hi, same problem here trying to install mutect 1.1.6. For me, the error seems to be related to the fact that maven repository changed from HTTP to HTPPS, there is an issue open in the mutect github but has no answer: https://github.com/broadinstitute/mutect/issues/13

  Any guidance on how to fix this or how to install these older versions of mutect? A precompiled jar file as mentioned would be ideal. In my case, I am trying to reproduce an analysis from a paper.

  Thanks for your help.

  Raquel

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  Genevieve Brandt (she/her)

  • August 19, 2020 19:44

  Hi Raquel Manzano, this is a very old version of the tool. Our support is focused on the newest releases, and we recommend that you use the newest version of GATK which includes Mutect2. Here is a link that may help you, but other than that, other community members who have successfully used this version may be able to help.

  For context, check out our support policy.

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  Raquel Manzano

  • August 20, 2020 08:45

  Hi Genevieve Brandt (she/her), I understand this is a very old version, I normally use mutect2 myself. I need to reproduce an analysis that was performed with this version of mutect, I'll try in the community otherwise I will just fix the code to use mutect2 then. Thanks a lot for your reply.

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  Nicole Saw

  • January 21, 2021 03:37

  Hi Raquel and Knight, 

  Did you manage to get that precompiled mutect 1.1.7 (or 1.1.6) jar file? I'm looking for this too!

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  Genevieve Brandt (she/her)

  • February 01, 2021 19:34

  Hi Nicole Saw,

  I am going to go ahead and tag Raquel Tobes and Knight Ni to see if they have any updates.

  Genevieve

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