I have a reference file
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?