我正在尝试使用 gatk VariantRecalibrator 重新校准我的 vcf,但不断收到错误“非法参数值:提供了位置参数”。但我不知道这意味着什么,或者如何纠正它!
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.
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我已阅读手册并尝试使用谷歌搜索,但看不到如何避免,非常感谢任何帮助!