Hi Rich,

That is consistent with the BED format, that is in "BEDs" 0 based coordinate system the SNP is at 1056309.   In the more common "1" based system this translates to 1056310.  If the end were inclusive the SNP would be at 1056309-1056310 in "BED" world,  that is it would take 2 positions.

The first base of a genome in BED coordinates is represented as  0-1.

My quick rule of thumb for converting between coordinate systems is to add (or subtract) 1 from the start base, leave the end base alone.

Jim

On Sun, Sep 11, 2011 at 10:58 PM, Richard Mark White <whiter3@yahoo.com> wrote:
Hi,
  This must seem like a newbie question but I cant get a clear answer.  My understanding from the galaxy wiki page http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_format is that all intervals in galaxy are 0 based, start inclusive end exclusive.  but when i use generate pileup/filter pileup and convert to intervals, i get something like this:
 
chr10 1056309 1056310 G C +

When i look up the SNP (G-->C) it is pretty clearly 1056310.  Which would make the "interval" end inclusive.  this is key because when i annotate snp's against dbSNP, i need to have the right cooridnates.

  Can anyone provide some guidance?  Thanks!

rich


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