Merging genotyping array VCFs and then running kinship analysis

Question

[Anupriya]

Hello,

I have about 4200 array genotyping VCFs (from the Illumina Infinium CoreExome-24 Kit) and I have merged them using bcftools merge. The chip has 500K exonic SNPs. These are trio data - which means 1700 of them are probands, mother and father respectively.

Following that, I converted them to Plink format using plinkv2 --make-bed function. I included the fam information later on by generating a fam file.

Finally, I ran KING --kinship but am getting a very high error rate for within family relatedness, which I know is not correct.

Are there other QC steps I should have been running at the merge step? I have removed all monomorphic SNPs and multi allelic sites, too.

Answer 1

[Jeremy Leipzig]

if you already have VCF try https://github.com/brentp/somalier