If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
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.
Exception thrown while running VariantRecalibrator
The command I am running is
gatk VariantRecalibrator -R /home/nick/Exome/reference/ucsc.hg19.fasta -input GRC14335721.vcf -recalFile GRC14335721.recal -tranchesFile GRC14335721_recalibrate_SNP.tranches -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /misc/exome/datasets/bundle/2.8/hg19/hapmap_3.3.hg19.sites.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /misc/exome/datasets/bundle/2.8/hg19/1000G_omni2.5.hg19.sites.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /misc/exome/datasets/bundle/2.8/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /misc/exome/datasets/bundle/2.8/hg19/dbsnp_138.hg19.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode SNP -l debug &> ../log/variant-recalibrator.log
and the debug output is in the attached log (scroll to the end to see error message). I thought maybe the execution was OK, but the generated recal and tranches files are empty.