VariantsToTable : Badly formed genome location

StevenSteven ParisMember
edited November 7 in Ask the GATK team

Hello,

I want to use VariantsToTable on a vcf files with Structurales Variations.
In my vcf, I have a translocation chr1:861936 => chr14:295688
But i have this error with this line :
Badly formed genome location: Parameters to GenomeLocParser are incorrect:The stop position 295688 is less than start 861936 in contig chr1

line in vcf :
chr1 861936 TRA006SUR N N[chr8:295687[ . PASS SVTYPE=BND;CHR2=chr8;END=295688

Do you have a solution?

Thank you,

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Answers

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin
    edited November 7

    Hi @Steven

    Would you please post the exact command, version of gatk and the entire error log.

    Thank you.

    Regards
    Bhanu

  • StevenSteven ParisMember

    Hi,

    command line :
    java -jar GenomeAnalysisTK.jar -T VariantsToTable -R ${FILE_REF_FASTA} -U ALLOW_SEQ_DICT_INCOMPATIBILITY --showFiltered -V ${PATH_WORKDIR_DIR}/${sample}/${sample}.SV.filtered.vcf -F CHROM -F POS -F END -F ID -F REF -F ALT -F FILTER -F STRANDS -F SUPP -GF GT -GF CO -o ${PATH_WORKDIR_DIR}/${sample}/${sample}.SV.filtered.txt

    gatk version :
    3.8-0-ge9d806836

    error log :

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.8-0-ge9d806836):
    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 https://software.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: Badly formed genome location: Parameters to GenomeLocParser are incorrect:The stop position 295688 is less than start 861936 in contig chr1

    If I do sed "s/END/FIN/" before the command line works.
    java -jar GenomeAnalysisTK.jar -T VariantsToTable -R ${FILE_REF_FASTA} -U ALLOW_SEQ_DICT_INCOMPATIBILITY --showFiltered -V ${PATH_WORKDIR_DIR}/${sample}/${sample}.SV.filtered.vcf -F CHROM -F POS -F FIN-F ID -F REF -F ALT -F FILTER -F STRANDS -F SUPP -GF GT -GF CO -o ${PATH_WORKDIR_DIR}/${sample}/${sample}.SV.filtered.txt

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