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

HaplotypeCaller interval list

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    HuixianXie

    Hello Leo, I met the same problem when I used the gatk HaplotypeCaller -- intervals command, it shows to me "A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chr16" is not valid for this input." 

    it's amazing~ I think my reference is complete and has the correct name, which should not appear. I have tried searching on the net and see that you have the same problem, but there is no solution.
    I have tried multiple times and see that my .dict file shows that Chr16-21, ChrX, and ChrY are vacant, I went back and looked at my reference genome and this does exist, I just need to recat the complete genome and try again.

    You can refer to my experience, good luck.

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