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  • Lilach
    Member
    • Sep 2011
    • 20

    #1

    Tabix for 1000 genomes

    Hi.
    I'm trying to use tabix for downloading variants from specific genomic regions, from the recently submitted phase 3 1000 genomes vcf files, here:
    ftp://ftp-trace.ncbi.nih.gov/1000gen...ease/20130502/

    for example, I tried:

    tabix –h ftp://ftp-trace.ncbi.nih.gov/1000gen...notypes.vcf.gz 3:43407818-43663560 > myfile.vcf

    but it did not work. I got:
    [tabix] the index file either does not exist or is older than the vcf file. Please reindex.

    of course, the ftp site contains the index file, and its date is later from the vcf file.

    This is the first time I'm trying to use tabix, and I don't know why it doesn't work?

    Thanks in advance.
  • Lilach
    Member
    • Sep 2011
    • 20

    #2
    I found the reason, so this question may be deleted.
    This was because I wrote long - instead of short - in the command line (because the command was written in Word and copied from there to the unix command line).

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