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.
-L option with PrintReads
I am using GATK-3.6 to analyze exome sequencing data. To speed up the analysis I split the BED file provided in GATK resource bundle (Broad.human.exome.b37.bed) into several files, one for each chromosome. I created the BQSR tables separately (in parallel) for each chromosome using the -L option. Under theses circumstances can I use the -L option with PrintReads to run on each BQSR table separately as well. It is not recommended in http://gatkforums.broadinstitute.org/gatk/discussion/4133/when-should-i-use-l-to-pass-in-a-list-of-intervals. The input to PrintReads file is a single deduplicated BAM file. Indel realignment is not performed