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CombineVariants --variants : can I give both a variant name and a file type?

JocelynSPJocelynSP Melbourne, AustraliaMember

I am trying to run tool CombineVariants on 3 vcf files.
There is an extra dot in the file names which I expect is why dynamic determination of type is not working.
I want to rename the variants, not have the default names of variant, variant1, variant2.

I can't seem to specify both variant-name, and file type. Can you explain how to combine them? In the meantime I can rename my files to a simpler format, but I would like to know! Below are error message for three attempts

Version with just variant-name:
% gatk -T CombineVariants \

-R $REFDIR/PlasmoDB-29_Pfalciparum3D7_Genome.fasta \
--variant:S3 D2_S3_indel.filterGff.vcf \
--variant:S4 E7_S4_indel.filterGff.vcf \
--variant:S5 G7_S5_indel.filterGff.vcf \
-o mergeS3S4S5.indel.vcf \
-genotypeMergeOptions UNSORTED

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):
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 'D2_S3_indel.filterGff.vcf' could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
ERROR Name FeatureType Documentation
ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)
ERROR ------------------------------------------------------------------------------------------

Version with --variants:VariantName:VCF vcf_filename:
gatk -T CombineVariants \
-R $REFDIR/PlasmoDB-29_Pfalciparum3D7_Genome.fasta \
--variant:S3:VCF D2_S3_indel.filterGff.vcf \
--variant:S4 S4_indel.filterGff.vcf \
--variant:S5 S5_indel.filterGff.vcf \
-o mergeS3S4S5.indel.vcf \
-genotypeMergeOptions UNSORTED
...

ERROR MESSAGE: Invalid argument value '--variant:S3:VCF' at position 4.
ERROR Invalid argument value 'D2_S3_indel.filterGff.vcf' at position 5.
ERROR ------------------------------------------------------------------------------------------

Version with --variants:VCF:VariantName vcf_filename:
gatk -T CombineVariants \
-R $REFDIR/PlasmoDB-29_Pfalciparum3D7_Genome.fasta \
--variant:VCF:S3 D2_S3_indel.filterGff.vcf \
--variant:S4 S4_indel.filterGff.vcf \
--variant:S5 S5_indel.filterGff.vcf \
-o mergeS3S4S5.indel.vcf \
-genotypeMergeOptions UNSORTED
...

ERROR MESSAGE: Invalid argument value '--variant:VCF:S3' at position 4.
ERROR Invalid argument value 'D2_S3_indel.filterGff.vcf' at position 5.
ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

  • JocelynSPJocelynSP Melbourne, AustraliaMember

    I tried removing the extra dot from the file name, and the type still could not be determined dynamically. The vcf files were not written by a GATK tool - they are from SNVer, manipulated using BEDtools. The error seems to be occurring before the file is read.

    % gatk -T CombineVariants -R $REFDIR/PlasmoDB-29_Pfalciparum3D7_Genome.fasta \
    --variant:1_S3 D2_S3_indelGff.vcf --variant:1_S4 E8_S4_indelGff.vcf \
    -o mergeS3S4_indel.vcf -genotypeMergeOptions UNSORTED

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):
    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 'D2_S3_indelGff.vcf' could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
    ERROR Name FeatureType Documentation
    ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
    ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
    ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)
    ERROR ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Can you post the header and a few records from the vcf file?

  • JocelynSPJocelynSP Melbourne, AustraliaMember

    The problem turned out to be that the header was missing. When I restored it, the type could be determined dynamically and I did not have to supply it.
    Also,
    --variant:variant_name,VCF filename.vcf
    is successful.

    Thank you.

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