Problem with ApplyRecalibration

mojaveazuremojaveazure MinneapolisMember

I'm trying to use ApplyRecalibration and I get the following error:

ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types

I validated it with ValidateVariants and got no errors wrong with the file:

Successfully validated the input file.  Checked 1592 records with no failures.

My code for the ApplyRecalibration is this

gatk -T ApplyRecalibration -R ucsc.hg19.fasta -input L7_Genotyped.vcf -mode SNP -recalFile L7.SNP.recal -tranchesFile L7.SNP.tranches -o L7.recal.SNPS.vcf -ts_filter_level 99.0

I'm using GATK 3.3.0, my supercomputing cluster doesn't have a newer version installed.

Every thing I've seen from the GATK team has been to validate the VCF file. I've done that and gotten no errors; the VCF file was generated using GenotypeGVCFs, so what's going on?

Answers

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    Where did you get your reference sequence from? Did it come with other files? Is it the one from the Broad/GATK resource directory from the ftp? Does your recal and tranches files exist? Was VariantRecalibrator run on the same input file? I'm not sure what is the problem. I have received that error myself, but I can't remember what was the problem back then.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Try deleting the VCF index file -- sometime it gets corrupted and causes this kind of issue. The next tool will regenerate an index automatically.

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