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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

How does Picard basecalling make decisions on NovaSeq data?

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    James Webber

    Hm. It's possible I'm just misreading some code in the lab (or the files were mislabeled/undocumented). Maybe Picard is not doing this after all?

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    Genevieve Brandt (she/her)

    Hi James Webber,

    I'm not sure exactly which Picard tool you are using. Could you fill in the details from here if you still want help from the GATK Support team?

    Thank you!

    Genevieve

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    James Webber

    I figured out was going on and it was unrelated to Picard. It was just using IlluminaBasecallsToSam and I thought it was producing these odd basecalls, but it was actually a downstream part of the pipeline I was using that was not initially obvious to me.

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    Genevieve Brandt (she/her)

    Okay, thanks for the update James Webber! Glad you found the issue.

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