The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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