I'm having problems with quality score recalibration using GATK as most tutorials/examples use an old version of GATK which has different syntax and arguments to the current version.
I have run this to get a recalibration table, which I think I need to get the recalibrated BAM files:
gatk-126.96.36.199/gatk BaseRecalibrator \ -reference human_genome/hg38_masked.fa \ --known-sites human_genome/All_20180418.vcf.gz \ --input S01_BAM_file.bam \ --output recal.table
This works fine, and I could run this for all of my samples.
But when I then do the next step to get the recalibrated BAM files I can't work out what to do.
*The old way of doing it was:
java –jar GenomeAnalysisTK.jar –T PrintReads \ –R human.fasta \ –I realigned.bam \ –BQSR recal.table \ –o recal.bam*
gatk-188.8.131.52/gatk PrintReads \ -R data_R3/human_genome/hg38_masked.fa \ --input S01_BAM_file.bam \ -**BQSR** recal.table \ --output quality_score_recalibrated_S01.bam
But this makes an error that says: "A USER ERROR has occurred: B is not a recognized option". And I can't find an alternative argument for -BQSR when I look at the PrintReads help manual.
Does anyone know the current way to run this quality score recalibration to get recalibrated BAM files?