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SelectVariants not accepting --variant

louwslouws San FranciscoMember
edited January 2015 in Ask the GATK team


I am attempting to run the tool SelectVariants and everything seems ok but for one error I receive:
##### ERROR MESSAGE: Invalid argument value '—-variant' at position 4.

##### ERROR Invalid argument value 'input.vcf' at position 5.

My intitial command was:

java -jar GenomeAnalysisTK.jar -T SelectVariants -R human_g1k_v37.fasta —-variant input.vcf -select '[my select code]' -o output.vcf

Any help appreciated.

Thank you!


Best Answer


  • louwslouws San FranciscoMember
    edited January 2015

    Brilliant tommycarstensen ! That was it. What a bizarre error, I never encountered it before. But your keen eye solved the problem. Thank you!

    edit: I should clarify for others who might have the same issue; the problem was the different dash sizes. Using a 'normal' dash size resolved the issue.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    For general information: we've seen this happen to people who write commands in a word processor (rather of text editor) and then copy/paste to console/terminal. Word processors will change some characters to be fancy -- they are just too helpful sometimes. Better stick with a simple text editor which won't try to do things you didn't ask for.

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