I have a .tgz file in which there are folders, one for each individual. Each folder contains vcf files, one for each chromosome. It's in this fashion: .tgz has ./individual1/chr1.vcf ./individual1/chr2.vcf etc, ./individual2/chr1.vcf ./individual2/chr2.vcf etc.
I want to create vcf files, one for each chromosome, containing individuals of a population using bcftools merge, so that later I can use the vcf files for an Fst estimation among populations using vcftools.
Having no previous experience for this kind of work, the only thing I can think is to extract the .tgz file, compress each vcf with bgzip and index it with tabix, run bcftools merge for each chromosome and population and finally run the Fst test on vcftools.
But is there a better way to do this? Extracting the .tgz file will chew up alot of storage space.
Thanks in advance.