Genome Analysis Toolkit

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

Could not find vcf.stats file after Mutect2

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    Anthony Dias-Ciarla

    Hi Seke Keretsu,

    Thank you for your much-appreciated patience and for writing to the GATK forum!

    I reviewed the error you encountered with our developers and received some feedback on your next steps.

    The cluster you are using doesn't seem to be saving your stats table properly when running the tool. Have you tried running the tool locally?

    I'd recommend the following: firstly, ensure that your stats table is, in fact, being generated. If it is being generated and isn't being saved, our hypothesis is likely correct. In that case, go ahead and re-try running the tool on your local computer instead of a cluster.

    I hope this helps! Please let me know if this leads you to success. If you have any further questions/issues in the meantime, please do not hesitate to reach out.

    Best,

    Anthony

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    Anthony Dias-Ciarla

    Hi Seke Keretsu,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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