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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

jar for mutect 1.1.7

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6 comments

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    Bhanu Gandham

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

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    Raquel Manzano

    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)

    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

    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

    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)

    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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