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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

VariantsToTable not extracting INFO 'sub-fields'

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    Genevieve Brandt

    Hi Francesco Mazzarotto, what you are attempting to do with VariantsToTable is not possible. We don't have a GATK tool that will do exactly what you want, but you could look into getting MAF output format from Funcotator and the results will be easier to manipulate into a table.

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    Shahryar Alavi

    But MAF output is somewhat different from VCF; and I think the VCF output format is better for germline variant annotation.

    With Funcotator we get an integrated (and minuter) "variant calling - annotation" workflow. But the problem is "vertical bar" separated INFOs are not easy for downstream text processing.

     

    I have two suggestions for the GATK Team:

    You may want to develop a new tool (like VariantsToTable) to separate each "sub-info" in the FUNCOTATION INFO, and put them into separate columns with corresponding headers when creating the tab-delimited table.

    Or add a feature to Funcotator to create multiple INFOs with FUNCOTATION prefix in their IDs; e.g.

    #INFO=<ID=FUNCOTATION_Gencode_34_hugoSymbol,...>
    #INFO=<ID=FUNCOTATION_Gencode_34_ncbiBuild,...>

    instead of

    #INFO=<ID=FUNCOTATION,...,Description="Funcotation fields are: Gencode_34_hugoSymbol|Gencode_34_ncbiBuild|...">

    Thanks

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    Genevieve Brandt

    Hi Shahryar Alavi,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

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