KING kinship inference error

Question

[ritafonsa]

Hello,

I'm trying to use KING for estimating kinship between individuals. I have a vcf file that resulted from a de novo assembly of ddrad seq data.

First, I tried to convert my vcf file to .bed file using Plink2.0, but it failed saying that human genome didn´t have that much chromosomes. I search a bit online and since my CHR column represents loci and not chromosomes I would have to include a letter on CHR ID. So I did add a "C" in the begging of every CHR ID and also used the flag -allow-extra-chr on plink.

I runned the following command:

./plink2 --vcf myfile.vcf --allow-extra-chr --make-bed --out one_snp

When I run KING:

./king -b one_snp.bed --related

I get the following error:

Read in PLINK bim file one_snp.bim...                                                              Genotype data consist of 0 autosome SNPs                                                         12469 other SNPs are removed.                                                                    PLINK maps loaded: 0 SNPs                                                                                                                                                                       FATAL ERROR -                                                                                    No autosome SNPs are available. Please check your map file.

I think the problem may be with the .fam file, but I'm not sure how to correct it since I don't have information on pedigree data. Is it necessary to run KING? Does anyone have any idea what is the problem?

Thanks in advance

[AMARU]

I came here two years later. Did you find a solution? I have the same issue now with post impute dataset. Thanks

Answer 1

[DBScan]

I've also tried that once, but wasn't successful as well. I ended up using SNPRelate R package, it provides relatedness inference (snpgdsIBDKING) as well (with KING algorithm). Conversion from VCF to GDS is very easy (snpgdsVCF2GDS).

Answer 2

[chrchang523]

KING does not include SNPs on scaffolds in its analysis. You have to lie to it and provide a .bim file that appears to only have regular chromosomes.

However, plink2 --make-king-table (https://www.cog-genomics.org/plink/2.0/distance#make_king ) does not have that limitation.