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error when convert human snp138.txt to .vcf format

bulashabulasha GermanyMember

I have used the following command $ java -jar GenomeAnalysisTK.jar -T VariantsToVCF -V:OLDDBSNP snp138.txt -R genome.fa -o snp138.vcf
to convert human snp138.txt file downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ to .vcf format.
As output the snp138.vcf file has been generated which has the size as 0 and the other 2 files have been generated as snp138.txt.idx and snp138.vcf.idx. How can i get the snp138.vcf?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Let's try to find out why the conversion didn't work. Can you please post the console output that was generated when you ran the command?

  • @Geraldine_VdAuwera
    when i am running
    java -jar GenomeAnalysisTK.jar -R mm10_genome.fa -T VariantsToVCF -V:OLDDBSNP snp142.txt -o dbsnp142.vcf
    I am getting the following error:

    ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file 'snp142.txt' 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 BEAGLE BeagleFeature (this is an external codec and is not documented within GATK)
    ERROR BED BEDFeature (this is an external codec and is not documented within GATK)
    ERROR BEDTABLE TableFeature (this is an external codec and is not documented within GATK)
    ERROR EXAMPLEBINARY Feature (this is an external codec and is not documented within GATK)
    ERROR RAWHAPMAP RawHapMapFeature (this is an external codec and is not documented within GATK)
    ERROR REFSEQ RefSeqFeature (this is an external codec and is not documented within GATK)
    ERROR SAMPILEUP SAMPileupFeature (this is an external codec and is not documented within GATK)
    ERROR SAMREAD SAMReadFeature (this is an external codec and is not documented within GATK)
    ERROR TABLE TableFeature (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)

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @RB_74
    Hi,

    It looks like .txt is not supported. Have a look at the tool doc for a list of file types that are supported.

    -Sheila

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