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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

MitochondriaPipeline on merged Bams

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    Valentin

    Hello Gatk-team Genevieve Brandt,

    so I figures the more important questions in this issue are:

    • Does the mitochondrial Pipeline work on merged bams? Is that tested or known?
    • Does it allow only one Read Group? In my merged bams there are two or more

    The answers to those questions should solve it. Now maybe another alternative if the pipeline doesn't work on merged bams, would be to make it run atomatically for larger sample numbers.

    So do you know of any way or maybe script that could make this Pipeline run for e.g. 20 Bam files (individually but) automatically?

    Thanks

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    Genevieve Brandt

    Hi Valentin, the MitochondriaPipeline is not written to handle merged bam files. Your error message is resulting from the WDL not expecting multiple values for the contamination output.

    You may want to check out our platform Terra, where you can easily batch run your 600 samples.

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    Valentin

    Thanks for the feedback Genevieve Brandt

    Terra requires a google billing account, to be linked to, right? I'm currently on that

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    Samantha Velasquez

    Hi Valentin,

     

    Yes, that's correct. You can find instructions on how to set up billing in Terra and linking your Google billing account to Terra here.

     

    Best,

    Samantha

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