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Error running FilterMutectCalls: alpha must be greater than 0 but got NaN

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    Genevieve Brandt

    Hi Larry S, thanks for writing in. Have you tried running one of your failed files using GATK 4.1.8.1 to confirm that it is still present in our newest release?

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    Larry S

    Hi Genevieve Brandt, thanks for getting back to me. Yes, I've tried version 4.1.8.1 as well and got the same error on a different bam file. I can try version 4.1.8.1 on all the files to confirm though. I'll have to do so tomorrow because the system is down for maintenance today. I'll get back to you tomorrow to confirm, but I'm pretty sure the error is also in 4.1.8.1.

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    Genevieve Brandt

    Thanks Larry S. I found a possible related open github issue ticket and reached out to the team for more info. Here is the link

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    Larry S

    Thanks Genevieve Brandt.  I'll follow the github link and this thread for any updates.

    Thanks again,

    Larry.

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    Larry S

    Hi Genevieve Brandt, I tried running the same analysis with the latest version of GATK, and wanted to confirm that the same error exists in version 4.1.8.1. 

     

    Thanks for your help,

    Larry.

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    Larry S

    Hi Genevieve Brandt,

     

    Has there been any update on this matter? I haven't seen a response on the github thread either. Any advice?

     

    Thanks,

    Larry.

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    Genevieve Brandt

    Larry S We are still looking into it, I'll let you know when I have updates.

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    Larry S

    Hi Genevieve Brandt. Thank you for the update. I'll follow this thread to see if there are updates.

     

    Thank you again,

    Larry.

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    Genevieve Brandt

    I opened a new issue ticket because it seems like a different issue than the previous issue I found. Here is the new link.

    I'll continue to let you know if there are any updates.

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    Larry S

    Thank you very much, Genevieve Brandt.

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    Genevieve Brandt

    Hi Larry S, could you upload your inputs to FilterMutectCalls in a bug report following these instructions so that we can debug the issue? Please also make sure to name the file folder something descriptive.

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    Larry S

    Hi Genevieve Brandt. I uploaded a tar file following these instructions: https://gatk.broadinstitute.org/hc/en-us/articles/360035889671. Look for the file: LarryS_FilterMutectCallsGeneratingNaN.tgz.  The shell script contains the commands I used.

    If there are problems please let me know.

    Thanks for your help,

    Larry.

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    Genevieve Brandt

    Thanks so much Larry S for getting that to us! We will continue to look into this issue.

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