Genevieve Brandt

@asalimih it looks like you're using a different tool than the original post in this thread. Could you post on the GATK forum to get help from the GATK support...

@daisyyr Thanks for posting your example here, this issue is still open so it has not been fixed yet.

@xmzhuo @twood1 we have released a fix for a very similar bug in Funcotator (#6289 ). Could you test the newest GATK version 4.2.3.0 and let us know if it...

Yes, I have asked the user to upload their data for testing.

Yes, I got the data today.

The user's uploaded data is named Joyce1NebulaFuncotatorAnnotated.vcf and Joyce1NebulaFuncotatorAnnotated.vcf.idx.

Someone from my team is going to give this issue a try, we'll post any updates here.

A similar error message has been reported on the forum [here](https://gatk.broadinstitute.org/hc/en-us/community/posts/360073781912-Error-when-running-HaplotypeCallerSparkinfinite). GATK Version: 4.1.9.0 The command is: ``` gatk# ./gatk HaplotypeCallerSpark -I HG03934.final.bam \ -O HG03934.final.g.vcf \ -R Ref/GRCh38_full_analysis_set_plus_decoy_hla.fa --emit-ref-confidence...

@jamesemery @lbergelson @cmnbroad It looks like this issue is persisting in the newest GATK version. I have asked the user for a file to replicate the issue and will update...