Argument with name 'BSQR' isn't defined

mjuliamjulia CanterburyMember


This is my first time trying to use the BaseRecalibrator tool and I don't know why I always get this error. I am running the following commands:

1.generate recalibration table:

java -jar /pathtogatk/GenomeAnalysisTK.jar -T BaseRecalibrator -R /pathtoref/ucsc.hg19.fasta -knownSites /pathtobundle/bundle/2.8/hg19/dbsnp_138.hg19.vcf -knownSites /pathtobundle/bundle/2.8/hg19/Mills_and_1000G_gold_standard.indels.hg19.vcf -I VCRI.fixmate.sort.fixindels.bam -o VCRI.fixmate.sort.fixindels.bam.recal_data.grp

2.plot data before and after recalibration:

java -jar /pathtogatk/GenomeAnalysisTK.jar -T BaseRecalibrator -R /pathtoref/ucsc.hg19.fasta -knownSites /pathtobundle/bundle/2.8/hg19/dbsnp_138.hg19.vcf -knownSites /pathtobundle/bundle/2.8/hg19/Mills_and_1000G_gold_standard.indels.hg19.vcf -I VCRI.fixmate.sort.fixindels.bam -BSQR VCRI.fixmate.sort.fixindels.bam.recal_data.grp -o VCRI.fixmate.sort.fixindels.bam.covar_table2.recal

3.generate the recalibrated bam file:

java -jar /pathtogatk/GenomeAnalysisTK.jar -T PrintReads -R /pathtoref/ucsc.hg19.fasta -I VCRI.fixmate.sort.fixindels.bam -BSQR VCRI.fixmate.sort.fixindels.bam.recal_data.grp -o VCRI.fixmate.sort.fixindels.fixartefacts.bam

The first one runs without any error, but both of the other ones always return this:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.4-46-gbc02625):
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Argument with name 'BSQR' isn't defined.
ERROR ------------------------------------------------------------------------------------------

Can anyone help me? What am I doing wrong?



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