I want to calculate kinship matrix for autosomes in order to run a LMM. For this purpose, I first pruned each autosome using bcftools (version 1.11) and excluded the snps that had r2 greater than 0.15 by utilizing the command:
/bcftools +prune -m 0.15 -w 1000 input.vcf -Ob -o output.vcf
When I use the file output.vcf for calculating the kinship matrix using Rvtests utilizing the command:
/vcf2kinship --inVcf output.vcf --bn --out kinship_output
I get an error: 'Wrong VCF header'
However, if I use the above command with input.vcf (i.e., the original file without pruning from the first command), the same command runs with the Rvtest and I get a kinship matrix. I assume while pruning, I am ouputting the vcf file in a wrong format. I have tried reading the bcftools tutorial but I have no clue where I am going wrong.