Tagged with #data processing pipeline
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Recent thread: http://gatkforums.broadinstitute.org/discussion/1677/best-practice-for-variant-calling-on-ion-torrent-data-with-gatk

Any progress on some Best Practices for data processing pipelines for variant detection with GATK on Iontorrent PGM/Proton data?

Any plans for GATK branches to deal with the particulars of IonTorrent output?