I am identifying new sequence variants/genotypes from RNA-Seq data. The species I am working with is not well studied, and there are no available datasets of reliable SNP and INDEL variants.
For BaseRecallibrator, it is recommended that when lacking a reliable set of sequence variants:
"You can bootstrap a database of known SNPs. Here's how it works: First do an initial round of SNP calling on your original, unrecalibrated data. Then take the SNPs that you have the highest confidence in and use that set as the database of known SNPs by feeding it as a VCF file to the base quality score recalibrator. Finally, do a real round of SNP calling with the recalibrated data. These steps could be repeated several times until convergence."
Setting up a script to run HaplotypeCaller and BaseRecallibrator in a loop should be fairly strait forward. What is a good strategy for comparing VCF files and assessing convergence?
