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Derek Caetano-Anolles

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Activity overview

Latest activity by Derek Caetano-Anolles
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    Derek Caetano-Anolles created an article,

    From GATK 4.1 to 4.2: Two years of updates in a nutshell

    It’s been over two years since we released GATK 4.1, so now is definitely the time to upgrade to GATK 4.2 if you haven’t opened up your bin directory since then. Our teams have worked tirelessly th...

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    Derek Caetano-Anolles created an article,

    GATK 4.2 release

    The latest GATK release is out, with changes corresponding to the period of October 10, 2020 - February 18, 2021. The full GATK release notes are available on the GATK GitHub, but here is just a ta...

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    Derek Caetano-Anolles created an article,

    GATK on the cloud with Azure

    We aim to provide the research community with a range of options for running our Best Practices workflows exactly the same way we do it in-house at the Broad Institute. To that end, we make all our...

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    Derek Caetano-Anolles created an article,

    GATK 4.1.9.0 release

    The latest GATK release is out, with changes corresponding to the period of June 20, 2020 - October 10, 2020. The full GATK release notes are available on the GATK GitHub, but here is just a taste ...

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    Derek Caetano-Anolles created an article,

    GATK 4.1.8.0 release

    The latest GATK release is out, with changes corresponding to the period of April 24, 2020 - June 19, 2020. The full GATK release notes are available on the GATK GitHub, but here is just a taste of...

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    Derek Caetano-Anolles commented,

    "I was thinking: should I exclude reads aligned to the pseudo genes of chromosome Y from the BAM files and then run the genotyping part of the pipeline to see if this makes a difference?" I don't t...

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    Derek Caetano-Anolles commented,

    So, if I'm understanding correctly, the depth for one of the y chromosome genes only has coverage in the male samples, which is what we should expect. That's good, but it doesn't tell us...

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    Derek Caetano-Anolles commented,

    Great! I'm glad it works! :)

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    Derek Caetano-Anolles commented,

    Hi Damian, I don't believe that HaplotypeCaller plays very nice with chrY, so it may be most expedient to just exclude them from the female analysis (if you're certain they don't actually have Y ch...

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    Derek Caetano-Anolles commented,

    The size of the index is determined by the number of bins, and in theory it should be optimizing itself for size, among other things. For what it's worth, 1.6MB can be the size of just the header, ...