Challenges Using KING for Relatedness Analysis with Non-Standard Genomes (8000 Chromosomes)

Question

[alex]

Hi everyone,

I am working on a project attempting to test the relatedness of around 100 individuals. We performed a de novo analysis using Stacks, and the resulting VCF file contains ~ 8000 "chromosomes" (contigs). My goal is to perform a relatedness analysis. I was attempting to use king but I have had issues converting such a large file into Plink binary format. I separated them into files of 95 chromosomes, converted, and then merged. However, the resulting king analysis excluded all of the samples.

Commands

$plink --vcf Test1.vcf --make-bed --out Test1 --allow-extra-chr --chr-set 95 no-xy --double-id 
$plink --vcf Test2.vcf --make-bed --out Test2 --allow-extra-chr --chr-set 95 no-xy --double-id 
$ plink --bfile Test1 --bmerge Test2 --make-bed --out MergedDataset --allow-extra-chr --chr-set 95 no-xy
$ ./king.exe -b MergedDataset.bed --kinship --minsnps 1 --prefix KinshipAnalysis

I then get this outcome The following 93 samples are excluded from the kinship analysis (M<512): (followed by all my samples).

My questions are then: Is king even suitable for this task? And if so what can I do to fix my issues? Or, are there alternative tools better suited for this kind of analysis?

Answer 1

[chrchang523]

1. With thousands of contigs, you should name your contigs 'contig1', 'contig2', etc. and use the --allow-extra-chr flag.
2. plink 2.0 has a --make-king-table command which may be sufficient for your needs.

[alex]

Thank you for your response, I will give it ago.

[alex]

Thank you, this worked perfectly!