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

Error in FilterMutectCalls

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    Tiffany Miller

    Hi Aditi, 

    I'm checking out your question now. First thoughts... the tool is expecting a numeric value in one of the inputs, but is finding a "." 

    Another user a while ago had this issue when using another tool before FilterMutectcalls - it replaced the MPOS tag in the vcf with "." Can you check your vcf? Also FYI, you forgot a dash in the -stats argument (i.e. --stats). This may be a bug, but give it a look and let us know!

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    Aditi Kulkarni

    Hi Tiffany,

     

    Sorry for the late response but I was doing some testing on my end. I was using a publicly available pipeline and that had a bug. So the issue was in the step that generates the VCF. Once I fixed that, this issue got fixed too.

    Thanks for your response.

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    Tiffany Miller

    No worries. We post our own public version of the best practice Mutect2 pipeline that we regularly test here and on the cloud platform Terra, if that is useful to you. 

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