Hi, I am trying to run the following command:
gatk VariantRecalibrator
-R genome.fa
-V all.Sample.SNP.vcf.gz
--trust-all-polymorphic -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.8 -tranche 99.6 -tranche 99.5 -tranche 99.4 -tranche 99.3 -tranche 99.0 -tranche 98.0 -tranche 97.0 -tranche 90.0 -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an SOR -an DP -mode SNP --max-gaussians 6
--resource hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz
--resource omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz
--resource 1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.hg38.vcf.gz
--resource dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz
--tranches-file output.tranches
-O output.recal
It gives me the following error message:
A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',hapmap_3.3.hg38.vcf.gz{1000G_omni2.5.hg38.vcf.gz{1000G_phase1.snps.high_confidence.hg38.vcf.gz{dbsnp_138.hg38.vcf.gz}' but no positional argument is defined for this tool
Can anyone help to resolve this issue?
Thanks
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