Bash script for calling CNVs using cnvkit
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??
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brunobsouzaa
1 answer
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;
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GenoMax
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brunobsouzaa
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Sorry guys, found the error.... No need to respond!
Post what the error was so it helps someone in future.