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GATK v4 Variant Recalibrator command line
Could someone please provide me with a sample command line to run Variant Recalibrator for GATK v4? I am running the tool using GATK 4 Alpha with the following command line:
~/gatk-protected/gatk-launch VariantRecalibrator -R ~/MiSeq/Bioinformatics/Archive/ReferenceFiles/hg19/seq/hg19.fa -input Stromal-combined-New.vcf --resource hapmap,known=false,training=true,truth=true,prior=15.0 ~/MiSeq/Bioinformatics/Archive/ReferenceFiles/GATK/hapmap_3.3.hg19.sites.vcf --resource omni,known=false,training=true,truth=true,prior=12.0 ~/MiSeq/Bioinformatics/Archive/ReferenceFiles/GATK/1000G_omni2.5.hg19.sites.vcf --resource 1000G,known=false,training=true,truth=false,prior=10.0 ~/MiSeq/Bioinformatics/Archive/ReferenceFiles/GATK/1000G_phase1.snps.high_confidence.hg19.sites.vcf --resource dbsnp,known=true,training=false,truth=false,prior=2.0 ~/MiSeq/Bioinformatics/Archive/ReferenceFiles/GATK/dbsnp_138.hg19.vcf -an DP -an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -an InbreedingCoeff -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -tranchesFile Stromal-combined-New.tranches --rscriptFile Stromal-combined-New.R
and I get the following error
A USER ERROR has occurred: Invalid argument '/home/galaxy/MiSeq/Bioinformatics/Archive/ReferenceFiles/GATK/hapmap_3.3.hg19.sites.vcf'.
The command syntax follows the same pattern as this
My Java version is java version "1.8.0_131"
Has the syntax been changed for GATK version 4?
Thank you very much.