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Searching bases in reference genome.

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  • Searching bases in reference genome.

    Is there a command line tool that would give me the nucleotide before and after a given mutation/variant base?

    Thanks
    -Kasthuri

  • #2
    You can use samtools to do this. i.e., samtools faidx REGION

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    • #3
      Great! Thanks. Well, for example, it is samtools faidx filename.fasta chr1:139266-139268 (to make it easy for folks who may have this question in future). Reference fasta should be indexed first using samtools faidx.


      -Kasthuri
      Last edited by kasthuri; 01-12-2012, 04:59 AM.

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