script.sh -i /storage/testFile
-i is stores path of /storage/testFile/
I want to iterate over file in testFile. Everything goes good, but I want to make this code more clean, add directory for output and other checks.
A snippet of my code is
for f in $inDir/*.vcf; do if [ -f $f ]; #check if file is true or exists then if [ ${f: -4} == ".vcf" ] # check if the file ends with .vcf then convert2annovar.pl -format vcf4 "$f" > ./"$f".avinput #run my code fi fi done
Issue:
echo $f I get /storage/testFiles/test.vcf
How do I get only test.vcf while I iterate in for loop?
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