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

CombineVariants Doesnt produce output

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    Anthony Dias-Ciarla

    Hi nroak,

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

    Firstly, could you please first clarify how exactly you produced these GVCFs? Did you use GATK or another tool? Where did these originate?

    Secondly, it would also be helpful if you could provide us with your vcf header. Specifically, we want the part of the vcf header that displays the types of each of the attributes. Please include all the info and format attributes in your vcf header.

    I look forward to hearing back from you!

    Best,

    Anthony

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