I want to use gatk-package-18.104.22.168 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-22.214.171.124-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