Question: Bash script for calling CNVs using cnvkit
0
gravatar for brunobsouzaa
18 months ago by
brunobsouzaa490
Brazil
brunobsouzaa490 wrote:

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??

software error • 334 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by brunobsouzaa490

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

ADD REPLYlink written 18 months ago by brunobsouzaa490

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

ADD REPLYlink written 18 months ago by GenoMax94k
0
gravatar for brunobsouzaa
18 months ago by
brunobsouzaa490
Brazil
brunobsouzaa490 wrote:

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;
ADD COMMENTlink modified 18 months ago by GenoMax94k • written 18 months ago by brunobsouzaa490
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