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Matt Snyder

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Latest activity by Matt Snyder
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    Matt Snyder commented,

    Hi Genevieve-Brandt-she-her, Sorry, I know this issue is ancient. I did use `--LENIENT_HEADER true` and just re-tried with Version:2.27.4-SNAPSHOT and got the same result. MAPPINGS_DIFFER, UNMAPPED...

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    Matt Snyder commented,

    Thanks, Genevieve-Brandt-she-her! I will try merging the bam files first. This also makes sense because then I only have to sort one BAM file instead of dozens. Do you have a recommended number of...

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    Matt Snyder created a post,

    markDuplicatesSpark running out of memory

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    Hi, GATK team and community! I am trying to process a large number of BAM files with MarkDuplicatesSpark run locally (without a spark cluster). These BAM files come from a very deeply sequenced WGS...

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    Matt Snyder created a post,

    picard CompareSAMs

    Answered

    Hi! I recently compared BAMs created with two slightly different version of a workflow and used picard CompareSAMs to compare the outputs. In my output tsv all *_DIFFER and MISSING_* are 0 yet ARE_...

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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...