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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.
BaseRecalibrator and per chromosome input bam files for a lane/sample
Hi I've a run my IndelRealigner stage per chromosome to speed up realignment runs as these can be quite time consuming (not via Queue) and thus have a bam file per chromosome for each lane/sample (as is discussed here http://gatkforums.broadinstitute.org/discussion/5996/ways-to-speed-up-indel-realinger), my question is: can I pass the ensemble of bam files to BaseRecalibrator with multiple -I arguments (assuming the engine will then present these files to BaseRecalibrator as a unified whole genome/lane(s)). Or will I need to merge my Indel realigned bams with Picard first into a single file before presenting these to BaseRecalibrator?