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| To use CNVkit on **amplicon sequencing data** instead of hybrid capture – **although this is not recommended** – you can exclude all off-target regions from the analysis by passing the target BED file as the “access” file as well: | To use CNVkit on **amplicon sequencing data** instead of hybrid capture – **although this is not recommended** – you can exclude all off-target regions from the analysis by passing the target BED file as the “access” file as well: | ||||
| > cnvkit.py batch ... -t Tiled.bed -g Tiled.bed ... | |||||
| ```shell | |||||
| cnvkit.py batch ... -t Tiled.bed -g Tiled.bed ... | |||||
| ``` | |||||
| This results in empty ”.antitarget.cnn” files which CNVkit will handle safely from version 0.3.4 onward. **However, this approach does not collect any copy number information between targeted regions, so it should only be used if you have in fact prepared your samples with a targeted amplicon sequencing protocol.** | This results in empty ”.antitarget.cnn” files which CNVkit will handle safely from version 0.3.4 onward. **However, this approach does not collect any copy number information between targeted regions, so it should only be used if you have in fact prepared your samples with a targeted amplicon sequencing protocol.** | ||||
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