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.
I'm now at the VQSR step of the best practices and to my surprise I got the following error related to java (I think):
Error: Could not find or load main class –jar
Here is my command line:
java –jar GenomeAnalysisTK.jar –T VariantRecalibrator –R ../human_g1k_v37.fasta –input ../raw_variants.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 ../hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 ../1000G_omni2.5.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ../dbsnp_138.b37.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 ../1000G_phase1.snps.high_confidence.b37.vcf -an QD -an MQRankSum -an ReadPosRankSum -an FS --maxGaussians 4 –mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 –recalFile raw.SNPs.recal –tranchesFile raw.SNPs.tranches -rscriptFile recal.plots.R
I don't understand what is the problem. Could someone look at it and identify if I made a mistake in my command line?
Thank you for your support