If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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


Sign In or Register to comment.