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Matt Snyder

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Latest activity by Matt Snyder
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    Matt Snyder commented,

    1. Community
    2. General Discussion
    3. picard CompareSAMs

    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, UNMAPP...

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    Matt Snyder commented,

    1. Community
    2. Other
    3. markDuplicatesSpark running out of memory

    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 ...

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    • Matt Snyder
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    Matt Snyder created a post,

    markDuplicatesSpark running out of memory

    Answered
    1. Community
    2. Other

    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...

    • Matt Snyder
    • 2 followers
    • 3 comments
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    Matt Snyder created a post,

    picard CompareSAMs

    Answered
    1. Community
    2. General Discussion

    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_...

    • Matt Snyder
    • Edited
    • 2 followers
    • 3 comments
    • 0 votes
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    Matt Snyder commented,

    1. Community
    2. Germline
    3. Insufficient variance error for VariantRecalibrator

    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,

    1. Community
    2. Germline
    3. Insufficient variance error for VariantRecalibrator

    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

    1. Community
    2. Germline

    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...

    • Matt Snyder
    • Edited
    • 2 followers
    • 5 comments
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    Matt Snyder commented,

    1. Getting Started
    2. Best Practices Workflows
    3. Germline short variant discovery (SNPs + Indels)

    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,

    1. Tool Index
    2. 4.1.7.0
    3. HaplotypeCaller

    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...