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HaplotypeCallerSpark stack overflow

Dear colleagues
All my attempts to use GATK HaplotypeCallerSpark with the option --spark-master local[*] fail because of stack overflow error with a similar error message as in https://github.com/broadinstitute/gatk/issues/5869
My GATK version is 4.1.2.0, that was installed via bioconda. On the github page describing the problem I have it is indiocated that this problem should be solved on Q2. Should I wait for the corrected version or is there a way to circumvent the problem with extra install or by using options like --java-options '-XssOptimalValue'?
When is the corrected version expected? Is Q2 (end of June?) still an option? Will it be readily on bioconda then?
Thanks
Thierry

Answers

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