How to give multiple input files to the gatk ?
I want to use gatk-package-220.127.116.11 for updating my VCF dictionary. I use the script below for just one VCF file, and it has worked so far.
java -jar gatk-package-18.104.22.168-local.jar UpdateVCFSequenceDictionary
-V /PATH _TO_INPUT_FILE.vcf --sequence-dictionary /PATH_TO_DICTIONARY.dict -O /PATH_TO_OUTPUT_FILE.vcf
Now I have multiple input files with different names. How should I change my script to update the dictionary of all files?
Thanks for any help
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