Calling Indels

[IonTom]

What do you think, is it possible to reliably call Indels using the Ion Torrent technology ?

From what i see in the data it seems more or less impossible.
Also quite a few people seem to share this opinion.

Bur there are some papers that claim that it is possible for short indels.
Also the torrent suite contains a tools for indel calling.

What are your experiences ?

[arnaud83]

It depends of your application.

For research, and with few genes it's possible but for clinical applications certainly not.

I realized some benchmarks to compare MiSeq and Ion Torrent technology (Ion Proton) and for indel there's no comparison between the two.

see attached file.

In red, MiSeq
in black, Ion Torrent

[snetmcom]

What do you think, is it possible to reliably call Indels using the Ion Torrent technology ?

From what i see in the data it seems more or less impossible.
Also quite a few people seem to share this opinion.

Bur there are some papers that claim that it is possible for short indels.
Also the torrent suite contains a tools for indel calling.

What are your experiences ?

Indel calling is not bad with their caller. The error profile is false positive indels in homopolymers, but their tools ignores most of these. It's pretty easy to rule those out anyways. I'm not sure how well it works for long indels though.