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 22.214.171.124:
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 \
Please could you confirm the current method used to generate the second recalibration table with GATK 126.96.36.199?
Unfortunately I could not identify the current method, including in the Base Quality Score Recalibration (BQSR) documentation.
Thank you for your time and help.
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