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  • TABIX on generic tab file

    Hi, Everybody,

    I have a 1-based, tab-delimited file with some annotations, which I would like to use with bcftools annotate on a vcf file.
    The fields are:
    CHROM, START, END, FEATURE, and a couple of more columns I am not really interested in.

    According to samtools 1.x instructions, the tab file needs to be bgzipped and indexed with TABIX.

    This is how I am proceeding:

    Code:
     bgzip myfile.tab # everything's fine so far
    and then:
    Code:
    tabix -s 1 -b 2 -e 3 myfile.tab.gz
    And that's when I get into trouble; the error I get is:
    [E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used?
    The offending line was: "CHROM FROM TO WIDTH STRAND FEATURE"
    Code:
    [E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used?
    The offending line was: "CHROM  FROM    TO      WIDTH   STRAND  FEATURE"
    I am a bit puzzled, what am I doing wrong?

    Thanks for your help,
    Max

  • #2
    use #CHROM FROM TO WIDTH STRAND FEATURE to mark it as a header line or just remove the line entirely.

    Comment


    • #3
      Thanks! I realize now it was a bit of a naive question, I'll do it straight away

      Best,
      Max

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