gatk vqsr --recal-file error

Question

[bioguy24]

In GATK 4.0.6.0 I am getting the below error using the command:

    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

Is that option not supported, I am following the best practices docs and think its correct or is there something else. Thank you :).

Answer 1

[Santosh Anand]

Probably the argument has been deleted as I could not find anything on the argument lists

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.3.0/org_broadinstitute_hellbender_tools_walkers_vqsr_VariantRecalibrator.php

Also, there is a thread on GATK reg. this and you may also like to follow there

https://gatkforums.broadinstitute.org/gatk/discussion/12449/gatk-4-variantrecalibrator-example-using-unavailable-option-recal-file

[bioguy24]

Thank you very much :).