Problem with ApplyRecalibration
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?