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MPetlj

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Latest activity by MPetlj
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    MPetlj commented,

    1. Community
    2. Somatic
    3. Mutect errors

    Hi Samantha: - Are the reference and dictionary files you are using the same version? I am not sure what are you refering to, but I ran this as a Terra workflow, to which we gave you the access and...

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    MPetlj commented,

    1. Community
    2. Somatic
    3. Mutect errors

      Update from GP re. the bam with error that formed 1 out of 9 failed jobs under discussion ('PAIR_29'; workflow ID: 633568d2-1bb4-47be-a655-a5b78e04f08e )  Mutect2 error was: Bam malformed, samtoo...

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    MPetlj commented,

    1. Community
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    3. Mutect errors

    All set, please let me know if you can see it. Thanks, Mia

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    MPetlj commented,

    1. Community
    2. Somatic
    3. Mutect errors

    Hi Samantha, Thanks for reaching out.  Your team already has an access to this workspace, called htapp-project/661-Clonal hematopoiesis. Please let me know if you can see this and if there is anyth...

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    MPetlj created a post,

    Mutect errors

    1. Community
    2. Somatic

    Hello,  I used Mutect2 Terra workflow to successfully call mutations in 232/241 samples.  Mutect2 version: mutect2:4.1.6.0 JobID: 45b78f7b-c418-47b5-bc64-f729602e6679 JobHistory: https://app.terra....

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    MPetlj commented,

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    3. Funcotator errors

    Hi Jason, Just an update: I removed the new variant that was failing and that seemed to have worked. So overall, two variants failed due to different reasons, it is not ideal, but it is OK. Of cour...

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    MPetlj commented,

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    3. Funcotator errors

    Hi Jason, I was rerunning the same workflow with the new vcf and new vcf.idx and now I get the following error:   The job ran further than the previous variant, but I still get the 'incompletely' ...

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    MPetlj commented,

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    3. Funcotator errors

    Thanks Jason, I will try that. Given that I need to modify the vcf and create a new index file, can you please let me know : 1.  is the workflow going to accept .vcf.gz.tbi index format ?  2.  if n...

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    MPetlj commented,

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    3. Funcotator errors

    Thanks Jason. I'd really appreciate every effort to help me resolve this by the end of this week as we have not been able to move these analyses anywhere forward for 3 weeks now (since the issue wa...

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    MPetlj commented,

    1. Community
    2. Somatic
    3. Funcotator errors

    Hi Jason, Thanks for addressing this with the team. I checked and there are no 'N' variants among the wild-type bases the VCF. In terms of the next variant in the input, following the last annotate...