Perform PCA for mtDNA MSA Data

Question

[Tastulek]

I tried to perform PCA on plink binary format data files which contained human mitochondrial genome data, but the analysis failed.

Are there any ways to prevent plink from excluding non-autosomes?

or

Do you recommend me any other programs/methods to perform PCA on mitochondrial data (i.e. haploid dataset)?

$ plink --bfile mtG_N2274 --pca 10 --out mtG_N2274

PLINK v1.90p 64-bit (16 Jun 2020)              www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to mtG_N2274.log.
Options in effect:
  --bfile mtG_N2274
  --out mtG_N2274
  --pca 10

4096 MB RAM detected; reserving 2048 MB for main workspace.
2726 variants loaded from .bim file.
2274 people (0 males, 0 females, 2274 ambiguous) loaded from .fam.
Ambiguous sex IDs written to mtG_N2274.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 2274 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.999847.
2726 variants and 2274 people pass filters and QC.
Note: No phenotypes present.
Excluding 2726 variants on non-autosomes from relationship matrix calc.
Error: No variants remaining.

[biosol]

Hi @Tastulek, I'm running on the same problem here. In this threads they suggest to convert the GT field of the vcf into a 0 and 1 matrix and to construct the PCA on that. However, I don't know what to do with heterozygous calls in the vcf (probably heteroplasmies?). Did you find a solution? Thanks in advanced!

[Tastulek]

Hello Biosol, I have not solved the problem yet. A colleague suggested me to convert haploid SNP calls of mtDNA into diploid homozygous, e.g. converting A into AA, G into GG, and so on, after that you can perform PCA on you mtDNA data as you do PCA on autosomal SNPs. However, I have not tried this myself... If you come up with a better solutions, please let me know...