Bash script for calling CNVs using cnvkit

Question

[brunobsouzaa]

Hi Guys, I'm using bash loop for calling CNVs between multiple samples using cnvkit. The loop is the following:

for i in $(ls *.Tumor.cnr | rev | cut -c 10- | rev | uniq)
do 
     cnvkit.py call ${i}.Tumor.cnr -y -m threshold -t=-2.0,-0.4,0.3,0.8,1.1,1.4,1.7 -o ${i}.call.cnr;
done;

But I'm getting the following error: sintax error near token'done'

Does anyone know what I'm doing wrong??

[brunobsouzaa]

Sorry guys, found the error.... No need to respond!

[GenoMax]

Post what the error was so it helps someone in future.

Answer 1

[brunobsouzaa]

Fixed error: The error was the missing ";" after "| uniq)"

for i in $(ls *.Tumor.cnr | rev | cut -c 10- | rev | uniq);
do 
     cnvkit.py call ${i}.Tumor.cnr -y -m threshold -t=-2.0,-0.4,0.3,0.8,1.1,1.4,1.7 -o ${i}.call.cnr;
done;