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Matt Snyder

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Latest activity by Matt Snyder
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    Matt Snyder commented,

    Hi again Pamela, I noticed that this helpful article points out that VQSR works best on cohort VCFs with at least 30 samples. In our organization we do not create cohort VCFs. Each VCF is only for ...

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    Matt Snyder commented,

    Hi Pamela, In the end it only works if I up the --max-attempts and drop the --max-gaussians. But it works! I am also running with "-mode BOTH", but the article you linked says "Note that VQSR must ...

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    Matt Snyder created a post,

    Insufficient variance error for VariantRecalibrator

    Hi im getting an error trying to test the VariantRecalibrator tool on a human sample.I'm using gatk v4.1.8.1.Here is my command with paths edited for privacy ;) gatk VariantRecalibrator \-R /qual_c...

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    Matt Snyder commented,

    This is super useful. However, none of the WDL workflows linked at the top actually use VariantRecalibrator or ApplyVQSR. It would be nice if there was an example workflow somewhere using these too...

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    Matt Snyder commented,

    I just ran HaplotypeCaller and got the error below. Clearly my input is not properly named. That is easily fixable and is not an issue.  A USER ERROR has occurred: Couldn't read file /home/dnanexus...