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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

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


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