Error: Failed to extract eigenvector(s) from GRM.
ManuelMoradiellos opened this issue · comments
Hi~!
I wanted to use Plink (v1.90b6.21 on Ubuntu 20.04.1 Linux x86_64) to obtain a Population Stratification PCA
of my variants dataset.
This dataset is a .tsv that I've tried to turn into a mock-up .vcf as input for plink, the .vcf headers are not exactly
real and I omitted including some information on various columns (QUAL, INFO) as they were a bit cumbersome
to add and as I thought that the Genotype (GT) information should be enough for my task.
I don't know if I'm missing something in the input .vcf or if I'm overlooking a command as I'm relatively new to
bioinformatics, but I include the .log and a fraction of the input .vcf if its any help.
Thanks in advance!!
99.5% of the genotypes in your input VCF are missing. PCA should not be used on variants with more than ~10% missing data.
Thanks, that was it! Here I was using a small subset as a toy example, but once I tried to apply it to my whole dataset I got what I asked for.
all.vcf.gz
Sorry to bother you, but I came across the same mistake：Failed to extract eigenvector(s) from GRM. I include the input .vcf if its any help.
Thank you very much!
Rerun --pca with plink 2.0; it will provide a more useful error message.
Thank you for your reply. After I deleted several samples with very high similarity with reference genes, the problem was solved