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

Haplotype caller error "Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class"


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    James Emery

    Hello Anna Gatseva. It appears you are running a very old version of GATK 4 (from 2018) on your machine and the stacktrace you are seeing appears to be associated with some depricated/removed codepaths in the code. We generally do not try to support older versions like this and it is It is highly likely that upgrading to a newer version should resolve this error.

    You can find newer GATK4 releases here: If you are still finding there are errors running the HaplotypeCaller on a newer release we would be happy to take a look and try to fix them for you. 

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