I run vcftools for multiple files, but when I use swiss army knife and use *, I get an error as it sees my input as extra arguments, instead of running it once for each file. Is there any way to avoid merging all the vcf files into one?
If you want to run Swiss Army Knife for multiple files, my idea for processing each file one by one would be to include there a for loopand iterate over each file, e.g.
for file in `ls *vcf.gz`; do vcftools ... done
Another approach to avoid merging would be to run a job per-file (using -iin flag, so it makes the computation in parallel and creates a new job for each input file).
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Hi Alexandros,
If you want to run Swiss Army Knife for multiple files, my idea for processing each file one by one would be to include there a for loop and iterate over each file, e.g.
for file in `ls *vcf.gz`; do vcftools ... done
Another approach to avoid merging would be to run a job per-file (using -iin flag, so it makes the computation in parallel and creates a new job for each input file).
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