Hi,
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
-T MuTect2
-R ready_bwa_reference_genome/hg19_complete.fasta
-I:tumor /pub6/GastricCancer/ZX/bam.ready/G01H.recal.bam
-I:normal /pub6/GastricCancer/ZX/bam.ready/G01N.recal.bam
--dbsnp known_sites_database/dbsnp_138.hg19.vcf
--cosmic known_sites_database/hg19_cosmic_v54_120711.vcf
--comp:hapmap known_sites_database/hapmap_3.3.hg19.sites.vcf
--comp:1000Genome known_sites_database/1000G_phase1.snps.high_confidence.hg19.sites.vcf
--comp:COSMIC known_sites_database/hg19_cosmic_v54_120711.vcf
-o GastricCancer/ZX/G01/G01_cosmic_mutect2.vcf
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?
Thanks
xiaolongge