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 work on Arabidopsis and now am running the BQSR. I have questions about the -knownSites option:
I have a population-level snp.vcf file which is quite large and I also have individual-level snp.vcf files. Should I use the population-level one or just choose one of the individuals? As the population-level snp file is quite large, I am worried it will slow down the process.
The indels and snps are included in a single file, should I separate them into independent files for the BQSR?