Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Problems with VariantAnnotator annotation (missing annotations)

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    Stefan Creadore

    I'm not exactly sure as I'm new to using GATK, but I did have a quick question in regards to annotations and was wondering if you could help me get started with using GATK to annotate since I'm not exactly sure where the best resource to learn is. I'd greatly appreciate it.

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    Aleš Maver

    It appears that removing INFO fields from the gnomAD vcf using 

    egrep -v "^##INFO=<ID=" gnomad.vcf > gnomad.fixed.vcf

    somehow solves the issue? Does this make any sense?

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    Bhanu Gandham

    Hi,

     

    Can you please share you vcf. We would like to recreate the error on our to help us debug. You can find info on sharing data with us here: https://gatk.zendesk.com/hc/en-us/articles/360035889671

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