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  • Kath
    Member
    • Nov 2010
    • 24
    #1

    Samtools - index

    Hello,

    I'm trying to use the SamTools index command. I have installed the latest version (0.1.9) but there doesn't seem to be an "index" in the SamTools folder. Instead there are "bam_index.c" and "bam_index.o". This is probably a stupid question but does anyone know the difference?

    Thanks

    Kath
    Tags: None
  • ntremblay
    Member
    • Dec 2009
    • 31
    #2
    Hi,

    have you tried from your terminal, samtools index xxx.bam? this should work to index your file if you have a compiled samtools executable ...

    if i'm not mistaken the bam_index.c and bam_index.o are the scripts used by your executable.

    hope that helps...

    Nicolas
    Nicolas Tremblay
    Graduate Student

    Cardiovascular Genetics - Andelfinger Lab
    CHU Ste-Justine Research Center

    Comment

    • Kath
      Member
      • Nov 2010
      • 24
      #3
      Ah ha, how right you are! Thanks.

      Comment

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