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Derek Caetano-Anolles

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Latest activity by Derek Caetano-Anolles
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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, ...

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    Derek Caetano-Anolles commented,

    Here is a description of how to use DetermineGermlineContigPloidy and GermlineCNVCaller to do the type of CNV analyses you are looking for. If you need more information, the DetermineGermlineContig...

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    Derek Caetano-Anolles commented,

    This is most likely an issue related to formatting or mismatches in read length between files. In Java, the ArrayIndexOutOfBoundsException is usually outputted when an index is passed to an array t...

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    Derek Caetano-Anolles commented,

    Using GenotypeGVCFs, it is normal behavior for a trailing field to be dropped if it is empty.So, if this is causing you issues downstream of your pipeline, a workaround would be to add a filler fie...