#This script checks read depth for each individual in the merged vcf file (as well as giving you number of sites) module load vcftools INPUT=/projects/cees/in_progress/angelimc/SNP_Calling_Rads/Italians/HaplotypeCaller_VCF OUTPUT=/projects/cees/in_progress/angelimc/SNP_Calling_Rads/Italians/Validate_VCF for f in $(cat $INPUT/list.txt); do vcftools --gzvcf $INPUT/${f}.vcf.gz --site-mean-depth -c > $OUTPUT/SiteMeanDepth_${f}.txt done