Using GATK we generated a vcf file and now using the following command, we have been trying to filter those reads. However, we observed little to no change in number of variants. I am unable to understand the problem Is there any error in the script below? Could you kindly suggest any other script or parameters to extract high quality snps
gatk VariantFiltration -R ref.fna -V raw.vcf -O filtered.vcf --genotype-filter-expression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --genotype-filter-name "my_filters"