We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

BQSR in GATK 4.0

hwewchanhwewchan Member
edited June 2018 in Ask the GATK team


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

Best Answer


Sign In or Register to comment.