Question: CNV calling on mapped IonTorrent reads
gravatar for graeme.thorn
14 months ago by
London, United Kingdom
graeme.thorn50 wrote:

I have circa 120 BAM files from IonTorrent Ampli-seq on the ThermoFisher Scientific Comprehensive Cancer Panel. Is the answer given in this question: CNV software for Ion Torrent data still relevant for calling CNV on the mapped results?

cnv • 295 views
ADD COMMENTlink written 14 months ago by graeme.thorn50

Is there not a plugin for CNV calling that can be used via the proprietary Ion Torrent software? If not, then, yes, CNVkit is still a valid tool. CNVkit was developed by the very guy who answered in that other thread.

Keep in the back of your mind, though, that the field is flooded with programs for detecting CNV from NGS data. Reproducibility across these programs is poor.

ADD REPLYlink modified 14 months ago • written 14 months ago by Kevin Blighe56k
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