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?