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.
How do I run BaseRecalibrator without known snps/indels
I am trying to run the BaseRecalibrator on plant data for which I have no SNP or INDEL data. The documentation clearly states that providing a set of known variants is OPTIONAL, but the program crashes. What is going on and how do I run the program without the SNPs which are not available? I have followed the pipeline given in the Best Practices and want to see it through.
Documentation for the tool:
States the following:
"--knownSites NA A database of known polymorphic sites"
However, I get this message:
ERROR MESSAGE: Invalid command line: This calculation is critically dependent on being able to mask out known variant sites. Please provide a VCF file containing known sites of genetic variation.
Should I simply not bother with this step and just run the Haplotype Caller? And will this yield equally good results?