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Rômulo Carleial

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Latest activity by Rômulo Carleial
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    Rômulo Carleial commented,

    1. Tool Index
    2. 4.2.6.1
    3. VariantFiltration

    "Filtered records will be preserved in the output unless their removal is requested in the command line."  At no point in the documentation you tell us how to request the removal. None of the argum...

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    Rômulo Carleial created a post,

    HOW TO EXCLUDE FILTERED VARIANTS WITH VARIANTFILTRATION?

    1. Community
    2. Documentation Questions

    Hi.  I am using GATK 4.2.6.1. I want to exclude the variants filtered with VariantFiltration, without having to run SelectVariants. My vcf file is 3TB heavy, and it makes absolutely no sense to pro...

    • Rômulo Carleial
    • 2 followers
    • 1 comment
    • 1 vote
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    Rômulo Carleial created a post,

    GATK GenotypeGVCFs stuck at starting traversal

    1. Community
    2. General Discussion

    Hi, I am trying to joint call SNPs using 5million BP intervals. My HPC only allows for 10d jobs, and calling intervals larger than that leads to failure (lack of time). I have managed to call 104 5...

    • Rômulo Carleial
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    Rômulo Carleial commented,

    1. Community
    2. Non-Human
    3. GATK GenotypeGVCFs stuck on starting traversal

    Hi Genieve. This is an old thread but GATK is giving me a lot of trouble with the same issue described above. Two 5million bp intervals are stuck at the traversal step. Last time it took GATK more ...