Test-drive the GATK tools and Best Practices pipelines on Terra
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A fatal error has been detected by the Java Runtime Environment when using MuTect2
I used MuTect2 for somatic SNV and indels calling and tested 9 tumor and matched normal WGS samples.
../jdk1.8.0_91/bin/java -jar ../GenomeAnalysisTK-3.6.jar
One sample worked successfully all the way:
But other samples was detected fatal JRE error at the end:
I want to know may I ignore the fatal JRE error because MuTect2 had finished it’s work and vcf.idx file had been created?