AnalyzeCovariates no option for second recalibration table

[GATKSupportTeam]

Summary

In the AnalyzeCovariates documentation, there is mention of the previous GATK3 method to obtain recalibration tables before and after BQSR. There does not seem to be that functionality in GATK4. If there is, it is not well documented.

User Request

This request was created from a contribution made by ISmolicz on February 17, 2021 12:03 UTC.

Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360077098031-Error-when-trying-to-generate-the-second-recalibration-table-for-AnalyzeCovariates

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Dear GATK Team,

In previous GATK4 versions, I understand there was a -bqsr option to use with BaseRecalibrator so that a second recalibration table could be generated and then submitted to AnalyzeCovariates. However, it appears this option is longer available as I receive the following error with GATK version 4.1.9.0:

A USER ERROR has occurred: -bqsr is not a recognized option.

The command used:

gatk BaseRecalibrator \
--input input.bam \
-R ucsc.hg19.fasta \
--known-sites dbsnp_138.hg19.vcf \
--known-sites Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
--known-sites 1000G_phase1.indels.hg19.sites.vcf \
-bqsr sample.recal_data.grp \
--output sample.recal_data_2.grp \
--tmp-dir $TMPDIR

Please could you confirm the current method used to generate the second recalibration table with GATK 4.1.9.0?

Unfortunately I could not identify the current method, including in the [Base Quality Score Recalibration (BQSR)](/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-BQSR- "Base Quality Score Recalibration (BQSR)") documentation.

Thank you for your time and help.

(created from Zendesk ticket #113534)
gz#113534