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wbsimey

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Latest activity by wbsimey
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    wbsimey commented,

    1. Community
    2. Documentation Questions
    3. Append GenomicsDBimport

    Thank you for the quick response Genevieve Brandt. I will create separate databases for the remaining chromosomes.

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    wbsimey created a post,

    Append GenomicsDBimport

    Answered
    1. Community
    2. Documentation Questions

    my version and error info:a) GATK version 4.2.0.0b) Exact command used: gatk --java-options "-Xmx200g -Xms200g" \GenomicsDBImport \--genomicsdb-workspace-path Neo_96_GATK_dbase \--batch-size 50 \-L...

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    wbsimey commented,

    1. Community
    2. Non-Human
    3. VariantFiltration undefined variable

    Hello Genevieve, It looks like the AB and MQ0 annotations are not here. When are these annotations created? I do not think I am doing anything different from previous GATK4 versions and I am using ...

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    wbsimey commented,

    1. Community
    2. Non-Human
    3. Selectvariants - specific region

    This worked: gatk SelectVariants \-R SBAPGDGG_D3.fa \-V gendb://../Tse_scaff_7_database \-L scaffold_7:97224243-97242568 \-O ../VCFs/output.scaff_7.vcf

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    wbsimey created a post,

    Selectvariants - specific region

    1. Community
    2. Non-Human

    a) GATK version used = 4.1.8   Hello, I  am  interested in selecting a specific region on a specific chromosome with SelectVariants (Chr9: 97,224,243 - 97,242,568) across all samples in my genomics...

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    • 2 followers
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    wbsimey created a post,

    VariantFiltration undefined variable

    Answered
    1. Community
    2. Non-Human

    Can you please provide a) GATK version used 4.1.8 b) Exact GATK commands used : gatk --java-options "-Xmx200g" VariantFiltration \     -R ../reference/SBAPGDGG_D3.fa \     -V ../VCFs/output.scaff_6...

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    wbsimey created a post,

    Haplotypecaller to GenomicDGImport and chromosomes

    1. Community
    2. Germline

    I am using GATK4 version 4.1.7.0 I searched the forum and did not find a similar question. I apologize if this is already answered.  I have a ref genome and 43 low coverage genomes with 23 chromoso...

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