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NextGenSeb 02-08-2012 03:28 PM

GATK and Ion Torrent data
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?


adaptivegenome 02-08-2012 06:30 PM

Take a look at this:

NextGenSeb 02-12-2012 08:36 PM

Very interesting blog, thanks for that!

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