How to save SNP table from GAP4?

Andrzej
2011-07-06
2013-04-18
  • Andrzej
    Andrzej
    2011-07-06

    Hello! I would like to save an SNP table from GAP4 from my assembly? Is there any way to do it…

    Do you know any other EASY to use software to take .ace, .caf files from MIRA to detect and SEE SNPs?

    Thank you,

     
  • James Bonfield
    James Bonfield
    2011-07-08

    This isn't easy to do in Gap4. The contig editor does have some very basic SNP reporting, but only if you've loaded a reference sequence and even then it's relatively untested code.

    If you can get your file into SAM format then there are a variety of SNP calling programs (eg samtools or some of the sam/bam graphical viewers). I'm sure there must be something that works natively off ace or caf too, but unfortunately I don't know of any.  I also don't know of any easy ways of converting ace/caf to sam except via importing to gap5 and exporting again, although this has the downside of probably changing the coordinates to include consensus columns that are pads. If there's a more direct and reliable way please let me know!

    Sorry I can't be of more help.

    James