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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

GatherVcfs to concatenate GVCFs

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    Anthony DiCi

    Hi sanjeevksh,

    Thank you for writing to the GATK forum! I hope that we can help you sort this out.

    Unfortunately, GatherVcfs (Picard) cannot concatenate GVCFs. The good news is that we have another GATK tool called CombineGVCFs that will do the job.

    Please give this tool a try and let me know if you find success. If any other questions arise in the meantime, please do not hesitate to reach out.

    Best,
    Anthony

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    Anthony DiCi

    Hi sanjeevksh,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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    sanjeevksh

    Hi Anthony (Anthony DiCi)

    Thank you for your feedback. I have used CombineGVCFs several times before for combining GVCFs from multiple samples but didn't realise it can be used for concatenating GVCFs as well. On this occasion, I have used GenotypeGVCFs on the per-interval generated GVCFs and converted the output vcfs into a single vcf using GatherVcfs but your feedback will be helpful going forward.

    Regards,

    Sanjeev

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