Hi all,

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
else
    cp -f temp.vcf temp2.vcf    
fi

PROBLEM: it creates the recode.vcf file but then the redirection is not happening as the temp2 file is empty

Any suggestions please