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.
BQSR in GATK 4.0
Thanks first for such a great tool! I have a question about BQSR in GATK 4.0 Best Practices.
In 3.8, PrintReads supports application of a covariates table file (with --BQSR) outputted from BaseRecalibrator tool along additional read-filtering options for preparing analysis ready BAM file. As stated in https://gatkforums.broadinstitute.org/gatk/discussion/2801/howto-recalibrate-base-quality-scores-run-bqsr#latest
In 4.0, is ApplyBQSR replacing PrintReads as the recalibration application steps? I see that PrintReads v4.0 is no longer support the --BQSR flag and ApplyBQSR supports --read-filter flag yet it is not very clear in the v4.0 best practices document that ApplyBQSR is the replacement. Please advise.
Thanks for your time