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java error in hmm accelerationof HaplotypeCaller, possibly a GATK bug?
Dear GATK team,
running the HaplotypeCaller with GATK 3.7, I recently got a reproducable java error which can be circumvented by disabling the pairHMM acceleration of HC by adding the --pair_hmm_implementation LOGLESS_CACHING option. I attach the log file of the error, here is the GATK command I used:
java -Xmx4g -jar GenomeAnalysisTK-3.7.jar -T HaplotypeCaller \
-R Homo_sapiens_assembly_GRCh38.fasta \
-L nexterarapidcapture_exome_targetedregions_GRCh38.bed \
-I mySample_MD_IR_BQSR.bam \
-o mySample_raw_variants.g.vcf \
--dbsnp dbSNP_b149_GRCh38p7.vcf \
-ERC GVCF -XA AF -ip 100