Question: CNV calling on mapped IonTorrent reads
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gravatar for graeme.thorn
7 months ago by
graeme.thorn40
London, United Kingdom
graeme.thorn40 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 • 224 views
ADD COMMENTlink written 7 months ago by graeme.thorn40

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 months ago • written 7 months ago by Kevin Blighe48k
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