GATK and Ion Torrent data

[NextGenSeb]

Hi all,

We have just started testing an Ion Torrent for variant detection in our lab, in order to compare it to other platforms. I am curious if anyone has tried using the PGM data in GATK? From memory GATK, or more specifically picard, does not like variable read length data. Moreover I would anticipate the comparatively low phred scores of Ion Torrent data to cause some trouble.

So, does anyone have experience/tips for the use of variable read length data in GATK, or suggestions for other software that would serve the same functionality as GATK?

Cheers
Seb

[adaptivegenome]

Take a look at this:

http://biolektures.wordpress.com/2011/12/10/ion-torrent-sequencing-on-humans/

[NextGenSeb]

Very interesting blog, thanks for that!