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