[maq-help] SOLiD SNPs

[Z R <a....@gm...>]

Hi Heng,
 Thanks for a wonderful tool. I am testing MAQ on a SOLiD dataset. As
described in one of the posts, I converted the reference to color space and
then align in color space.
My questions are after that step:
1) Can I use the color map to assemble and create the consensus (maq
assemble) or do I have to convert to the nucleotide map and then assemble.
2) I want to use cns2cssnp, which means I need 'in.color.cns' as one of the
arguments to the program. Again, does this imply that in.color.cns was
generated by using 'maq assemble' with the color space map?
3) On running cns2cssnp I get something like

   346     AA       GG          20      5
   456      CC       TT           30      7

and so on. As you say in the manual, cns2cssnp only gives the positions of
the SNP's and does not show the actual nucleotide substitution. How do I get
the actual nucletide substitution?

Again, thanks you for MAQ and for all the help.

Andrew.