Here is the code that gets the VCF file from a specific region using `tabix` and then filters it for specific (european) population using 'keep' option from vcftools.
#select specific population
if [ "$POP_FILE" != "" ]; then
vcftools --vcf temp.vcf --keep $POP_FILE --recode --recode-INFO-all > temp2.vcf 2> /dev/null
cp -f temp.vcf temp2.vcf
PROBLEM: it creates the recode.vcf file but then the redirection is not happening as the temp2 file is empty
Any suggestions please,,,