Hello All

I generated vcf file using GATK (First Haplotypecaller --> CombinedGVCF --> GenotypeGVCF and then Hard filtering ). After this, I converted filtered vcf file into plink binary PED files (.bed, .fem, .bim, plink v1.9) using --make-bed command. However, when I used these files for ROH detection using --bfile and --homogyz command, It showed 0 ROH.

Please help me to resolve this issue.

Thanks