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Extracting REF and ALT from VCF

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  • Extracting REF and ALT from VCF

    This may be a simple question.

    I am trying to extract CHR, POS, REF and ALT and other info from a VCF file to a txt file using vcftools. Can somebody point me how to get REF and ALT? I don't get this information but everything else.

    Thanks
    -K.

  • #2
    I think vcf-to-tab does exactly that:
    vcf-to-tab < file.vcf

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    • #3
      Originally posted by id0 View Post
      I think vcf-to-tab does exactly that:
      vcf-to-tab < file.vcf
      Thank you, id0. It works and I get the genotypes. But I don't get other information from the FORMAT fields. I know I can use --extract-FORMAT-info separately and 'paste' these two lists, but I would be more comfortable if I can get the genotypes as well as the format fields information at the same time. Anyway, I thank you for the solution.

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      • #4
        Originally posted by kasthuri View Post
        Thank you, id0. It works and I get the genotypes. But I don't get other information from the FORMAT fields. I know I can use --extract-FORMAT-info separately and 'paste' these two lists, but I would be more comfortable if I can get the genotypes as well as the format fields information at the same time. Anyway, I thank you for the solution.
        Also, I will be just happy with the ALT entries instead of actual variants. Is it possible to get that?

        Thanks
        -K.

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        • #5
          vcf's are naturally text files. If yours isn't, it's just compressed, so uncompress it.

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          • #6
            Originally posted by swbarnes2 View Post
            vcf's are naturally text files. If yours isn't, it's just compressed, so uncompress it.
            Thank you swbarnes2. I found VariantsToTable in GATK does exactly what I wanted.

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