customize SAM/BAM format

[plichel]

Hi,

I want to analyse 454 data that cover exonic as well as intronic regions. Is it possible to hold this information in the bam and sam files ?
I could imagine to either (i) label each sequence position with a char, telling whether the position is in a exon or intron or (ii) have some string saying 1-100:intron;101-400:exon. I think the first way would provide better flexibility and is easier to read, but would consume more file size.
I also looked in the sam/bam doc but I didnt find any possibility to customize.

So is it possible to simply add my own fields into the sam and bam ? Would this recognized by the samtools sam/bam parsers ?

Thanks,
plichel

[drio]

You certainly can. The SAM specification has reserved fields for end users (check X? - page 6 of the spec).

I wouldn't recommend that though. I would keep everything in one BAM and parse
it as necessary. You can also consider having multiple BAMs containing the alignments
that match certain filters.