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

converting multisample vcf to fasta



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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.

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    Hi William Brown

    First, it is incorrect to call such data transformation as conversion. The data in VCF and fasta are nonequivalent.  Second, googling can help. There is the same question on biostars ( with answers. I guess the best option is to use BCFtools (see this page for exact commands for your query You can also use

    You can handle multisampling manually in a script wrapper which selects one sample out of an array of samples and creates a single-sample VCF for it, followed by running any of the above-mentioned tools.

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