Question: CNV calling on mapped IonTorrent reads
gravatar for graeme.thorn
7 weeks ago by
London, United Kingdom
graeme.thorn30 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 • 129 views
ADD COMMENTlink written 7 weeks ago by graeme.thorn30

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 7 weeks ago • written 7 weeks ago by Kevin Blighe39k
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