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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.
Polysolver: input BAM question
Is there any advantage in launching the pipeline with a whole-genome bam? I was thinking that pulling out from the original BAM unmapped reads plus reads mapped to the HLA-locus could be ok and make the step "getting matching tags" much much faster. Would that be ok?