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BaseRecalibrator error

Hi everybody,

I am using gatk 4- BaseRecalibrator tool in my pipeline, and the following is my commands:


export dbSNP=/reference/hg37/dbsnp_138.b37.vcf
export Gold=/reference/hg37/Mills_and_1000G_gold_standard.indels.b37.vcf
export G1000=/reference/hg37/1000G_phase1.snps.high_confidence.b37.vcf
export REF=/GRCh37.fasta

gatk BaseRecalibrator -I $BAM/$PREFIX.sorted.bam -R $REF --known-sites $dbSNP --known-sites $Gold --known-sites $G1000 -O $RECAL/$PREFIX.recal_data.table

and I got the following error:
A USER ERROR has occurred: Invalid argument '/reference/hg37/dbsnp_138.b37.vcf'.

May anyone help me in that?

Answers

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