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Old 02-08-2012, 03:28 PM   #1
NextGenSeb
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Default 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?

Cheers
Seb
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Old 02-08-2012, 06:30 PM   #2
adaptivegenome
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Take a look at this:
http://biolektures.wordpress.com/201...ing-on-humans/
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Old 02-12-2012, 08:36 PM   #3
NextGenSeb
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Very interesting blog, thanks for that!
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gatk, ion torrent, variable read length, variant calling

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