Bash looping over files in different directories and print output

Question

I have *.vcf , *.vcf.vcfidx and *.vcf.idx files in directory /mypath/mydir/ . I want to loop over .vcf files only using command below (for file 1):

command for one vcf file:

vcf-subset -c sample.txt vcffile1.vcf | bgzip  -c > output_vcfile1.vcf_.vcf.gz

Can someone please help loop over all the .vcf (not vcf.vcfidx or vcf.idx ) files and get the output for each file in designated directory /get/inthis/dir/ using the command shown above?

Answer 1

Just use glob pattern *.vcf :

for i in *.vcf; do echo "$i"; done

The glob pattern *.vcf will match only files ending in .vcf .

Your command:

for i in *.vcf; do
    vcf-subset -c sample.txt "$i" | bgzip  -c > /get/inthis/dir/output_"$i"_.vcf.gz
done

---

If you have to search for .vcf files in a specific directory eg /foo/bar/ , do:

for i in /foo/bar/*.vcf; do
    vcf-subset -c sample.txt "$i" | bgzip  -c > /get/inthis/dir/output_"${i##*/}"_.vcf.gz
done