This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Challenges Using KING for Relatedness Analysis with Non-Standard Genomes (8000 Chromosomes)

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?

vcf relatedness
• 1,870 views • link
written by alex • alex

1 answer

  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.
• 0 views • link
written by chrchang523 chrchang523

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

• 0 views • link
written by alex • alex

Thank you, this worked perfectly!

• 0 views • link
written by alex • alex

Log in to answer this question.

More posts like this