VCF error in GATK-SV joint-calling terra pipeline, 18-SVConcordance step
Hello, I've resolved the error in my previous post here by running bigger batches of size 100. Now proceeding with the pipeline, I'm running into an error at step 18-SVConcordance. The error is
htsjdk.tribble.TribbleException$InternalCodecException: The allele with index 2 is not defined in the REF/ALT columns in the record.
The VCF causing this is the output from step 16-RefineComplexVariants, named cpx_refined.vcf.gz. What does this error indicate?
Please let me know if I need to provide anything else for debugging purposes, thank you!
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For any future users encountering this issue, it was addressed in the comment thread here https://gatk.broadinstitute.org/hc/en-us/community/posts/33681801704347-Error-in-GATK-SV-joint-calling-terra-pipeline-07-FilterBatchSites-step
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