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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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 . . .