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Hapmap to VCF

ykhedikarykhedikar SASkatoonMember

I work with plant species. I have a hapmap file and want to convert it to VCF file using GATK.
I am using following codes but getting error.

java -Xmx2g -jar /projects/gbs_bin/gatk/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -R genome.fa -T VariantsToVCF -o output.vcf --variant:RawHapMap snp.hapmap

java -Xmx2g -jar /projects/gbs_bin/gatk/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -R genome.fa -T VariantsToVCF -o output.vcf --variant:RawHapMap SNP.hapmap -et NO_ET

what is GATK 'key file' and --dbsnp 'dbsnp.vcf '?

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):


ERROR This means that one or more arguments or inputs in your command are incorrect.

ERROR The error message below tells you what is the problem.


ERROR If the problem is an invalid argument, please check the online documentation guide

ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.


ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions


ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.


ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see for more information and instructions on how to obtain a key.




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