jar for mutect 1.1.7
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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Here is a list of all the GATK releases: https://github.com/broadinstitute/gatk/releases
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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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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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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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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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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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