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I 'm trying to bootstrap a set of known variants of my 100 non-human data. And I followed the steps from this passage : https://software.broadinstitute.org/gatk/documentation/article?id=11081
It says , First do an initial round of variant calling on your original, unrecalibrated data. Then take the variants that you have the highest confidence in and use that set as the database of known variants by feeding it as a VCF file to the BaseRecalibrator.Finally, do a real round of variant calling with the recalibrated data. These steps could be repeated several times until convergence. But there's something I don't understand.
I have already done an initial round of variant calling on my original data and used some of these sites to do a round of BQSR. And I saw "These steps could be repeated several times until convergence". So I'm wondering if I want to repeat it which step to begin with ？ Use the new BAM files to call variants forming a new vcf file as knownsites or just feed BAM files as input files to BaseRecalibrator?