Visual distinction between syn/non-syn mutations

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What version of the product are you using? On what operating system?

0.22

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index.html lists all the SNPs with their "annotation". For CDS features you 
list the amino acid change eg. M189V. The majority of SNPs will be synonymous 
(eg. P281P), and are of less interest than non-syn ones. However the non-syn 
ones are difficult to find in the big lists.

Could you highlight these in some way to distinguish them from syn ones?

Or even better, create different tables for the different SNP types?
eg. syn, non-syn, intergenic.

Original issue reported on code.google.com by torsten....@gmail.com on 4 Jan 2013 at 3:40

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Two answers:

1) I'd be fine with highlighting them. Perhaps in bold and a different color 
for the text showing the amino acid change would be enough?

2) If you want different tables, you could post-process the "annotated" genome 
diff file located in "output/evidence/annotated.gd).  Ideally our command like 
this would work, but there appears to be a bug with that (it's not something we 
regularly use -- I'll investigate):

gdtools FILTER -m SNP -o output.gd -f snp_type=nonsynonymous annotated.gd

Anyway, all you'd have to do is grep for "snp_type=nonsynonymous".

You can annotate an unannotated GD file (like output/output.gd) or generate 
HTML table-like output (without alignments) from any genome diff file with a 
command like this (which should be in working order):

gdtools ANNOTATE [--html] -o output.html -r reference.gbk input.gd

Original comment by jeffrey....@gmail.com on 4 Jan 2013 at 10:22