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Krithika_Subramanian

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  • GATK Germline CNV calling

    Answered
    1. Community
    2. General Discussion

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: GATK-4.1.8.0b) Exact command used: Followed this post workflow (https://gatk.broadinstitute.org/hc/en-us/articles/360035...

    • Krithika_Subramanian
    • 3 followers
    • 4 comments
    • 0 votes

  • GATK Variant Filtration undefined variable

    1. Community
    2. Germline

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.0b) Exact command used: gatk VariantFiltration -V Input_SNP.vcf -filter "QD < 2.0" --filter-name "QD2" -filter "QU...

    • Krithika_Subramanian
    • 2 followers
    • 7 comments
    • 0 votes

  • GenomicsDB incremental error

    1. Community
    2. Germline

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.4.1b) Exact command used: gatk GenomicsDBImport -V S1_Haplotypecaller.g.vcf -V S2_Haplotypecaller.g.vcf -V S3_Haplot...

    • Krithika_Subramanian
    • 3 followers
    • 5 comments
    • 0 votes

  • GATK-CollectVariantCallingMetrics - regarding more information

    1. Community
    2. Documentation Questions

    Can you please provide a) GATK version used : 4.1.2.0b) Exact GATK commands used : gatk CollectVariantCallingMetrics \       INPUT=${input_vcf} \       OUTPUT=${metrics_basename} \       DBSNP=${d...

    • Krithika_Subramanian
    • 2 followers
    • 1 comment
    • 0 votes