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

VCF - Variant Call Format Follow

4 comments

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    Loren Cassin Sackett

    The last paragraph says "This is how people used to do variant analysis on large numbers of samples, but we do not recommend proceeding this way because that workflow suffers from serious methodological flaws." Could you please explain or link to a document that explains these methodological flaws? 

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    ISmolicz

    As Loren Cassin Sackett has mentioned, it would be useful to have a further explanation. If it is not advised to combine VCFs for multiple samples, what would be the recommended method to compare variants in separate VCFs for multiple samples after variant calling, filtering and annotation has been completed?

    Thank you for your help.

    Kind regards.

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    lid.zigh

    Hello, 

    I have the same question too.

    "If it is not advised to combine VCFs for multiple samples, what would be the recommended method to compare variants in separate VCFs for multiple samples after variant calling, filtering and annotation has been completed?"

    Could anyone answer to this question? 

    Thank you.

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    Lynn Fink

    Is support planned for 5-methyl-cytosine bases in the VCF format? I am currently performing an accredited NGS methylation clinical assay on cancer specimens, sometimes in combination with an NGS genetic clinical assay on the same patient, and I would like to combine the output from both assays into a single VCF. I have base-resolution for the CpG sites I interrogate, but I can't see that the VCF format supports bases outside of A,C,G,T, and N so I don't know how to encode that information.

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