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VQSR --recal-file not reconized

cmccabecmccabe ChicagoMember

In gatk is the --recal-file option not required or has it been changed? Applyvqsr uses this recal-file, but will that throw an error? Thank you very much :).

    gatk VariantRecalibrator \
        -R /home/cmccabe/Desktop/fastq/resources/ucsc.hg19.fasta \
        -V NA12878.vcf.gz \
   --resource hapmap,known=false,training=true,truth=true,prior=15.0:/home/cmccabe/Desktop/fastq/resources/hapmap_3.3.hg19.sites.vcf.gz \
   --resource omni,known=false,training=true,truth=false,prior=12.0:/home/cmccabe/Desktop/fastq/resources/1000G_omni2.5.hg19.sites.vcf.gz \
   --resource 1000G,known=false,training=true,truth=false,prior=10.0:/home/cmccabe/Desktop/fastq/resources/1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz \
   --resource dbsnp,known=true,training=false,truth=false,prior=2.0:/home/cmccabe/Desktop/fastq/resources/dbsnp_138.hg19.vcf.gz \
   -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \
   -mode SNP \
   --recal-file /home/cmccabe/Desktop/fastq/NA12878.recal \
   --tranches-file /home/cmccabe/Desktop/fastq/NA12878.tranches \
   --rscript-file /home/cmccabe/Desktop/fastq/NA12878.plots.R

A USER ERROR has occurred: recal-file is not a recognized option


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