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Begonia_pavonina

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Latest activity by Begonia_pavonina
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    Begonia_pavonina commented,

    1. Technical Documentation
    2. Glossary
    3. Spanning or overlapping deletions (* allele)

    As Degang Wu and Sam Khalouei I encounter several difficulties with the spanning or overlapping deletion allele notation (*). It is not recognised by downstream analysis tools, in my case the ANGSD...

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    Begonia_pavonina commented,

    1. Tool Index
    2. 4.1.3.0
    3. GnarlyGenotyper (BETA)

    I decided to use GnarlyGenotyper instead of GenomicsDBImport, as the number of genotypes for this last one is limited to 50. A GATK team member as advised to use GnarlyGenotyper in the link below. ...

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    Begonia_pavonina commented,

    1. Tool Index
    2. 4.0.10.0
    3. GenomicsDBImport

    GenomicsDBImport seem to freeze when used with reference genome with numerous or larger scaffolds/pseudo chromosomes. I got an user error related to the number of intervals which was above 100. I h...

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    Begonia_pavonina commented,

    1. Community
    2. Non-Human
    3. Access to outdated forum discussion

    Hello Genevieve, it is great to have kept old post in the Legacy GATK forum! Thanks for the link!

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    Begonia_pavonina created a post,

    Access to outdated forum discussion

    1. Community
    2. Non-Human

    Hello everyone, I am currently working on variants recalibration for non-model organism. I have found this really nice website that describe the method step-by-step. https://evodify.com/gatk-in-non...

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    Begonia_pavonina commented,

    1. Technical Documentation
    2. Algorithms
    3. Variant Quality Score Recalibration (VQSR)

    This link is broken: The human genome training, truth and known resource datasets that are used in our Best Practices workflow applied to human data are all available from our Resource Bundle. A li...

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    • 1 vote
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    Begonia_pavonina commented,

    1. Community
    2. Germline
    3. VariantFiltration ReadPosRankSum & MQRankSum undefined

    Argh, too bad the link is broken now! Would you have any other link to the answer?

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