README.md

README.md

@@ -59,7 +59,9 @@ Many fully sequenced genomes, including the human genome, contain large regions
 
 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.**