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
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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