Hello!

I have a reference file

x.vcf.gz

I also have multiple query files say

1y.vcf.gz

2y.vcf.gz

3y.vcf.gz

.... 603y.vcf.gz

I want to intersect the reference with each separate query file.

Since I have the query files all in one folder, I did

for i in *.vcf.gz; do bcftools isec $i /mnt/projects/x.vcf.gz -p $i -n =2 -w 1; done

This generated multiple folders called 1y.vcf.gz 2y.vcf.gz 3y.vcf.gz.

If I don't specify -p it will just overwrite the files.

Each of these folders contain files with the same name.

Is there any way to simply just rename the files with a prefix and not create multiple folders?