Hi all! I am following GATK best practices tutorial to perform the clean up of a DNAseq dataset of a non model organism (whole genome of a single individual). Everything was going ok until I arrived to the Base recalibration step (BSQR).
If there isn't a trustworthy SNPs databse available yet (which is my case), this is what GATK recommends: You can bootstrap a database of known SNPs. Here's how it works: 1-First do an initial round of SNP calling on your original, unrecalibrated data. 2-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. 3-Finally, do a real round of SNP calling with the recalibrated data. These steps could be repeated several times until convergence.
Can anyone provide further details on these steps? (the second step in particular).
Kind regards. Luciano