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Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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

Kind Regards


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