VariantsToVCF

rzengrzeng HoustonMember
edited October 2013 in Ask the GATK team

I am doing with mouse exome sequencing and met the error when I convert .txt snp database to .vcf format using VariantsTOVCF
the commands I used are as follows,

$ java -jar GenomeAnalysisTK.jar -R genome.fa -T VariantsToVCF --variant:mm10 snp137.txt -o snp137.vcf

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.7-4-g6f46d11):
ERROR
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
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
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:

Answers

  • rzengrzeng HoustonMember

    I redid it by using modified commands as follows, It works this time but snp137.vcf file is empty or size as 0.

    $ java -jar GenomeAnalysisTK.jar -T VariantsToVCF -V:OLDDBSNP snp137.txt -R genome.fa -o snp137.vcf

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    There might be a formatting issue in your dbsnp file. Did you get this file straight from a repository or from someone else?

  • rzengrzeng HoustonMember

    Thank you for the reply, Geradine, I got this file from Illumina index file package. Seems like it does not work easily jut by convert it to VCF format.

    I have downloaded another VCF file from Sanger and found that the variant VCF format file is not compatible with the reference file when I run GATK basecalibration.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    the variant VCF format file is not compatible with the reference file when I run GATK basecalibration.

    You need to make sure that you're using the same genome build to align your reads as was used to generate the dbsnp file.

  • rzengrzeng HoustonMember

    the genome.fa is an indexed file based on build mm10 that I downloaded from Illumina and the variant VCF format file is based on build mm10 too that I downloaded from Sanger.

    When I look at the each file carefully and found that the order of chromosome of genome.fa is different from VCF file, I am trying to find a tool to sort VCF file according to genome.fa, but it did not work though.

    Thank you,

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Have you tried vcsorter? It's not our tool so I can't provide support for it, but I believe others have used it successfully.

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