Bash script for pairwise comparisons

Question

I would like to write a bash script to do a pair calculation with my files.

I have a fixed file in a directory and a number of files that I want to use for pairwise comparisons.

For instance:

The name of the fixed file: Genome.vcf The name of the files for pair computing, which are in the same directory: ind_GER, ind_ENG, ind_MRO

I came up with the following script:

#!/bin/bash

for pop1 in $(find ind_*)
do
for pop2 in $(find ind_*)
do

 vcftools --gzvcf PATH/Genome.vcf --weir-fst-pop $pop1 --weir-fst-pop $pop2 --out $pop1_$pop2_fst

done
done

The error I am getting is:

Error: Requested Missing Argument

Obviously, something is wrong with me, I would be very grateful if you could help with this, thanks.

Answer 1

Change this:

--out $pop1_$pop2_fst

for

--out ${pop1}_${pop2}_fst

_ is a valid character in the variable name.