I am running Mutect2 (us.gcr.io/broad-gatk/gatk:22.214.171.124) on Terra using in PON mode for a single hg38 WGS CRAM. I have cloned the example Terra workspace and updated the reference info and all somatic workspace files to hg38, but am having a problem with Funcotator. It looks like Funcotate isn't properly handling the case where the variant is close to the start of the contig and is making the start of the reference window negative rather than the start position of the contig. The log file is too large to post in its entirety, but here is part of the error with Funcotate:
java.lang.IllegalArgumentException: Invalid interval. Contig:chrUn_KI270468v1 start:-1 end:18
I have tried increasing memory with no change to the tool behavior. I would like to get to the bottom of this issue. I have asked a similar question on the Terra forum and was referred here as it seems to be an issue with the functionality of the Funcotator tool.
Would appreciate any help getting to the bottom of this.
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