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variantRecalibrator-command not found

Yuan1109Yuan1109 NetherlandsMember

Dear all,

After I used vctutils.pl to filter the SNPs, Im trying to run variantRecalibrator to recalibrate the SNPs. I run the command line as follow:
java -Xmx4g -jar /data/home/yuan/HiCD12/GATK/GenomeAnalysisTK.jar
-T VariantRecalibrator
-R Nvit_2.0.linear.fa
-input HiCD12_fil_variant.vcf
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf
-resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf
-resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.vcf
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_135.b37.vcf
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff
-mode SNP
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0
-recalFile HiCD12_fil_variant.recal
-tranchesFile HiCD12_fil_variant.tranches
-rscriptFile HiCD12_fil_variant.plots.R

AND got EEROR:
variantRecalibrator.txt: line 2: -T: command not found
variantRecalibrator.txt: line 3: -R: command not found
variantRecalibrator.txt: line 4: -input: command not found
variantRecalibrator.txt: line 5: -resource:hapmap,known=false,training=true,truth=true,prior=15.0: command not found
variantRecalibrator.txt: line 6: -resource:omni,known=false,training=true,truth=false,prior=12.0: command not found
variantRecalibrator.txt: line 7: -resource:1000G,known=false,training=true,truth=false,prior=10.0: command not found
variantRecalibrator.txt: line 8: -resource:dbsnp,known=true,training=false,truth=false,prior=2.0: command not found
variantRecalibrator.txt: line 9: -an: command not found
variantRecalibrator.txt: line 10: -mode: command not found
variantRecalibrator.txt: line 11: -tranche: command not found
variantRecalibrator.txt: line 12: -recalFile: command not found
variantRecalibrator.txt: line 13: -tranchesFile: command not found
variantRecalibrator.txt: line 14: -rscriptFile: command not found

So where is the problem?
Thank you in advance.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    edited October 2016

    @Yuan1109
    Hi,

    It looks like you may have too many spaces/too many lines between the arguments. Try simply having one space between all the arguments. Also, can you confirm if you type java -jar GenomeAnalysisTK.jar --help you get some list of tools and descriptions?

    Thanks,
    Sheila

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