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

How do I get output v4.3 VCF file?



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    Bhanu Gandham

    Hi ,

    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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    Hi Melissa Nel

    You are not alone with this problem. However, the differences in latest VCF formats are minor I dare to say. Could you please specify the tool you are using which requires VCF v4.3 format? Anyway, I am 90% sure that the problem is not actually a problem and everything can be solved by changing the very first VCF header entry from




    The tool you want to use precautiously prohibits the usage of older VCF versions which is definitely not a good idea given the format differences between the latest VCF specs. 

    Changing the entry in a VCF header can be made via bcftools reheader or plain sed (not a good idea if you have a large VCF).

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