gatk VariantRecalibrator 位置参数错误

Question

我正在尝试使用 gatk VariantRecalibrator 重新校准我的 vcf，但一直收到错误“非法参数值：提供了位置参数”。但我不知道这是什么意思，也不知道如何更正！

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：

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

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.

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

我已阅读手册并尝试使用谷歌搜索，但看不出如何避免，非常感谢任何帮助！

Answer 1

本例中的错误消息令人困惑。 --resource 参数格式不正确，额外的白色 space 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称而不是用 space 分隔。

即

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

GATK Forum 是获得此类问题答案的好地方。

gatk VariantRecalibrator 位置参数错误

gatk VariantRecalibrator positional argument error

gatk