RFC: Providing a way to convert Illumina manifests to BED?

[lbeltrame]

I post this as I wrote something similar to handle our custom amplicon workflows. Perhaps it would be interesting to have such a thing?

[chapmanb]

Luca;
This sounds cool, although I don't practically know anything about Illumina manifests. Ideally we'd have this upstream of the main run as a template extension functionality that does the conversion as part of the preparation. This would help maintain a distinction between preparation (where we have lots of special cases) and the running (where we'd like to limit special cases so have everything be more robust). How would that work?

[lbeltrame]

This sounds cool, although I don't practically know anything about Illumina
manifests. Ideally we'd have this upstream of the main run as a template

Neither did I, I found out by reading the MiSeq manuals. ;) IMO it only makes
sense for regional or exome data sets, where you have to define the regions
you're interested in.

Manifests are ini-like CSV files. I only implemented this part because I saw a
discrepancy with what the instrument did (I don't need that stuff, but you
know...) and the regions I calculated myself. The format at least for amplicon
studies is somewhat documented in Illumina's manuals.

(where we have lots of special cases) and the running (where we'd like to
limit special cases so have everything be more robust). How would that
work?

I think it makes perfect sense.

[lpantano]

closing this since it seems Brad suggestion worked.

thanks a lot!!!!