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?
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.