GATK : VariantRecalibrator no positional argument is defined for this tool.
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11 months ago
Dr.Animo ▴ 10

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

GATK filtration Variant SNP • 859 views
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Hi, did you solve this problem? i faced the same problem two days ag0, but i sitll not solve it til now, so i want to know whether you done it well! thank you very much! i am grating to hear from you!

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yes, I have solved it. The following vdauwera comment help me to solve this.

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11 months ago
vdauwera ★ 1.2k

You’re using an outdated syntax for the resource argument, the latest docs show the following:

--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.sites.vcf.gz \

See https://gatk.broadinstitute.org/hc/en-us/articles/4405443709595-VariantRecalibrator

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