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.

Is fixmate necessary after alignment by BWA-mem? Which attributes of the reads are fixed by fixmate?

Is fixmate necessary for a bam resulting from BWA-mem alignment (i.e. before we apply gatk (picard)'s Remove duplicate and base recalibration to it)? Which attributes of the reads are fixed by fixmate?

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