GATK GenomicDBImport missing argument --intervals for Illumina HiSeq Exome??
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5 months ago
yussab ▴ 30

Hi everyone,

I'm using the GATK germline short variant discovery (SNPs + Indels) pipeline.

https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-

After using HaplotypeCaller to call the GVCF, I'm not consolidating the variants using GenomicsDBImport. https://gatk.broadinstitute.org/hc/en-us/articles/360036883491-GenomicsDBImport

This tool ask as a requirement "--intervals", as, "One or more genomic intervals over which to operate".

I'm calling variants from Illumina HiSeq Exome, so I probably need a .bed list of Exomes.

I didn't find any similar resource in the GATK bundle, but maybe I just missed it?? https://console.cloud.google.com/storage/browser/genomics-public-data;tab=objects?forceOnObjectsSortingFiltering=false

Thank you very much in advance,

Youssef

gatk exome GenomicDBImport illumina • 239 views
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