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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.
Differences between BQSR pipeline in two different GATK documents
I noticed that the pipeline for BQSR is slightly different between the "Workshop walkthrough (Brussels 2014)" document and the "(howto) Recalibrate base quality scores = run BQSR" document. I used the former document as my guide since it is more recent, but I am curious as to why these two are different. The first step is the same for the 2 docs, but then for the second step, the output is a recal.bam file in the brussels document instead of a post_recal.table file in the (howto) document. Then, I am confused about the (howto) document because it seems that the 4th step is exactly the same as the second step, except we generate a recal.bam file. Is the brussels document presenting steps that are more efficient? (since there is only 1 use of -BQSR to generate the recalibrated bam file we need, as opposed to 2 uses of the option)