I'm trying to use recalibrate my vcf using gatk VariantRecalibrator, but keep getting an error "Illegal argument value: Positional arguments were provided". But I don't know what this means, or how to correct it!
Here's my call:
gatk VariantRecalibrator \
-R "/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/Homo_sapiens_assembly38.fasta" \
-V "$OUT"/results/variants/"$SN".norm.vcf.gz \
-AS \
--resource hapmap,known=false,training=true,truth=true,prior=15.0: "/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/hapmap_3.3.hg38.vcf.gz" \
--resource omni,known=false,training=true,truth=false,prior=12.0: "/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/1000G_omni2.5.hg38.vcf.gz" \
--resource 1000G,known=false,training=true,truth=false,prior=10.0: "/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/1000G_phase1.snps.high_confidence.hg38.vcf.gz" \
--resource dbsnp,known=true,training=false,truth=false,prior=2.0: "/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/Homo_sapiens_assembly38.dbsnp138.vcf" \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \
-mode SNP \
-O "$OUT"/results/variants/"$SN".norm.vcf.gz.output.AS.recal \
--tranches-file "$OUT"/results/variants/"$SN".norm.vcf.gz.output.AS.tranches \
--rscript-file "$OUT"/results/variants/"$SN".norm.vcf.gz.output.plots.AS.R
And the error I see:
***********************************************************************
A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/hapmap_3.3.hg38.vcf.gz{/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/1000G_omni2.5.hg38.vcf.gz{/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/1000G_phase1.snps.high_confidence.hg38.vcf.gz{/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/Homo_sapiens_assembly38.dbsnp138.vcf}' but no positional argument is defined for this tool.
***********************************************************************
I've read the manual and tried googling, but can't see how to avoid, Any help much appreciated!
The error message in this case is confusing. The --resource arguments aren't formatted correctly and extra whitespace is causing it to interpret the following arguments as positional arguments.
The problem is that --resource blocks should have the meta information attached to the argument name instead of separated with a space.
i.e.
--resource:hapmap filename instead of --resource hapmap: filename
The GATK Forum is a good place to get answers to questions like this.