gravatar for Tastulek

3 hours ago by

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.



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