I have faced with a problem in filtering my vcf file, I am quite stuck. I have tried several options but none of them worked out. I want to do filtering at the "sample level" and keep only those with DP >=10. I have tried in VCFtools --minDP flag and --maxDP are not working!
I have tried all of these codes, non of them working
vcftools --vcf myfile.vcf --minDP 10 --recode --out out_1.vcf bcftools filter --soft-filter 'FMT/%DP>10' my.file.vcf`
does anyone has any solution for this problem?