gatk VariantRecalibrator位置参数误差

Question

我试图使用gatk重新校准我的vcf，但始终得到一个错误“非法参数值:提供了位置参数”。但我不知道这意味着什么，也不知道如何纠正它！

这是我的电话：

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

我看到的错误是：

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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.

***********************************************************************

我已经阅读了手册，尝试过谷歌搜索，但无法看出如何避免，任何帮助非常感谢！

Answer 1

本例中的错误消息令人困惑。--resource参数的格式不正确，额外的空格导致它将以下参数解释为位置参数。

问题是--resource块应该将元信息附加到参数名，而不是用空格分隔。

即

--resource:hapmap filename而不是--resource hapmap: filename

GATK论坛是一个很好的地方来获得这样的问题的答案。