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 have bovine next generation sequence results from illumina miseq platform. In the data I have specific three genes. I need to do variantrecalibration, first what would I need to do this analysis? In the example command line, all the data sets origin is human since I am working with "nonhuman organism" I don't have every file on the list.
What information from the file would be essential for the VariantRecalibration step?
Also, I don't have the vcf file but one could be generated from the bovineHD SNP , so the generated file from bovineHD array manifest would be suitable to use for next generation sequence variantrecalibration analysis?