I understand that snp array is better for proving relatedness, but we have 2 vcfs generated from exom data, and we need to show if there is any relatedness between them.
I tried these two commands from vcftools and both get the same output:
vcftools --vcf p1p2.vcf --relatedness vcftools --vcf p1p2.vcf --relatedness2
The output is:
INDV1 INDV2 RELATEDNESS_AJK P1 P1 -nan P1 P2 -nan P2 P2 -nan
Any hint why I am getting nans?