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Generating Recalibrated .bams after making the initial truth set for non-model organisms
I'm working with a non-model organism that does not have a database of SNPs like dbsnp. I have made the "initial truth set" by hard filtering my variants using VariantFiltration. I generated a table using BaseRecalibrator using my .vcf created from the VariantFiltration and my .bam file. Is the next step to generate a recalibrated .bam using ApplyBQSR with my original .bam file and the table generated using BaseRecalibrator? And then continue with base recalibration and variant calling . . .