Question: Relatedness inference using KING
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gravatar for sara.aglantarek
4 months ago by
sara.aglantarek10 wrote:

Hi everyone! I need some help on KING. I have a multivcf, containing informations about a certain number of trios and I want to confirm the relationship of the trios: so parent-proband = 1st degree, parent-parent = unrelated/2nd degree (if they're consanguineous) etc...

I have the pedigree file which I created from scratch and looks like this: ped file https://drive.google.com/open?id=1-oJFXZH7jCN1VBz1dKHyND3KhBmuHmhf

I tried to run king without calling the pedigree file and this is what I get using this command:

king -b multisample.bed --related --degree 2

kinship inference

https://drive.google.com/open?id=1KVaM_iCnlTnCEV88gAHEjM-bY64Cd9B8

I would like to use the new pedigree file using king, but I don't know how to do this, but on KING's manual there's nothing about it.

Thank you very much in advance.

ADD COMMENTlink modified 4 months ago by zx87549.2k • written 4 months ago by sara.aglantarek10

Ok I understand that from the ped and the map file I have to create the binary ped (bed, bim, fam). I tried to do this but I get this error:

Error: Line 1 of .ped file has fewer tokens than expected.

But the ped file has exactly the 6 mandatory columns that should have. How can I solve this problem?

ADD REPLYlink written 4 months ago by sara.aglantarek10

Unfortunately, there are two different types of .ped files; .ped + .map pairs require the .ped file to contain pedigree and genotype information.

Instead, try plink2 --vcf <VCF filename> --fam <pedigree-only .ped filename> --make-bed. (This requires plink 2.0.)

ADD REPLYlink modified 4 months ago • written 4 months ago by chrchang5236.9k
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