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GATK BaseRecalibratore Error

Hi everybody I have started to analyze exome data through GATK pipeline. I have run this commands , however, i took this message 

for f in *marked_duplicates.bam; do java -Xmx17G -jar /home/apps/gatk/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar  BaseRecalibrator  -I $f -R /home/hg19/ hg19.fa --known-sites /home/hg19/snp/ dbsnp_138.hg19.vcf -O ${f/.bam/.grp} ; done

A USER ERROR has occurred: Illegal argument value: Positional arguments were pro vided ',hg19.fa{dbsnp_138.hg19.vcf}' but no positional argument is defined for this tool.

It should be appreciated if you let me know your coments.

next-gen
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written by daffodil • daffodil

Dear Pierre Thanks a lot It is done:)

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written by daffodil • daffodil

Then accept @Pierre's answer (green checkmark) to provide closure to this thread.

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written by GenoMax GenoMax

1 answer

remove space in ' /home/hg19/snp/ dbsnp_138.hg19.vcf' (=> /home/hg19/snp/dbsnp_138.hg19.vcf )

same for option /home/hg19/ hg19.fa => /home/hg19/hg19.fa

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written by Pierre Lindenbaum Pierre Lindenbaum

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