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.
Could not find walker with name: "RealignerTargetCreator" and "BaseRecalibrator"
Please find the below code and the error I am getting. I tried all the versions 3.4 to 3.8.1 but I couldn't figure it out. The same error is happening with "BaseRecalibrator " as well, Please let me know the resolution for this problem.
[email protected]:~/Satish$ java -Xmx4g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -o Exome_sample_RG_index.marked.bam.list -I Exome_sample_RG_index.marked.bam -known dbsnp_138.hg19.vcf -L nexterarapidcapture_expandedexome_targetedregions.bed