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I have a bash script:

I am wondering how I can change this script to loop over a bunch of .vcf files and give output .txt with the name of corresponding .vcf

I tried changes done in similar script in Changing this code in a way to work for my files but I just messed everything up

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If we save the script pasted in the main post as a sh file and we have some .vcf files in a folder, by this line we can iterate over vcf files to extract what mentioned in the script returning .txt output by the name of corresponding vcf

for file in *.vcf ; do bash indel_vcf_parasing.sh $file ; done

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  • $\begingroup$ Can you provide some context to future readers about this answer $\endgroup$ – Bioathlete Jan 6 at 14:50
  • $\begingroup$ This is generally the method I use for scaling. Write a program to do 'one', then write wrappers, or use one-liners (as this answer shows) to do many. You will need to be sure that successive runs do not step on each other (if using a single directory for all runs), or make a new directory for each run if necessary. $\endgroup$ – Scot Jan 6 at 18:57
  • $\begingroup$ Please edit your answer to include the extra details so the answer is complete and a user doesn't have to read all the comments to understand. $\endgroup$ – Bioathlete Jan 7 at 15:08
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Error means that quotations are missing. I am not going to review this chunk but at first glance check

printf 'TumorAltAlleleCount\tTumorAltAlleleFrequency\t'\n'

There are three quotation marks so one is not matched. I suggest you develop code within a good IDE that will help you debug. Please google around for potential solutions. I personally do R and Shell scripting in RStudio. It differently colors quoted and unquoted code so you immediately see if you missed a closing quotation somewhere.

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