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

MergeVcfs issue: Illegal character in fragment at index 1: ##fileformat=VCFv4.2



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    Anthony DiCi

    Hi Liyang Zhang,

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

    To start, it looks like the .list file contains multiple file names. Within one of the VCF paths in this interval list file, there is likely a character that is not legal in the URI. I suggest searching for any weird characters in the URI. GATK seems to be choking on the file name rather than the actual contents of the file.

    I hope this helps! Please let me know what you find. Feel free to reach out with any further questions in the meantime.


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    Hi Liyang, how did you resolve this? Thanks

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