hello all,
i am trying to plot the PCA values for our GWAS study using plink. below is the code used and results:
plink --vcf local_chr2.vcf.gz --maf 0.001 --indep-pairwise 50 5 0.2 --vcf-half-call missing --out chr2-clean plink --vcf local_chr2.vcf.gz --genome gz --out local_chr2.vcf-2 --vcf-half-call missing --extract chr2-clean.prune.in plink --vcf local_chr2.vcf.gz --extract chr2-clean.prune.in --pca var-wts --vcf-half-call missing --out chr2-clean
the chart from the R code is below
pcs = read.table( "~/Desktop/chr2-clean.eigenvec" ) plot( pcs[,3], pcs[,4], xlab = "PC1", ylab = "PC2" )
then i went on to compare the PCA values against the 1000 genome. for this I merged the the two vcf files using bcftools using the following code: bcftools merge *vcf.gz -Oz -o Merged.vcf.gz
when running the plink PCA command on the merged version i got an empty PCA plot
plink --vcf Merged.vcf.gz --extract chr2-clean.prune.in --pca var-wts --vcf-half-call missing --out merged.with.1000G
any help on what i did wrong? i am so confused? is it because i used bcftools to merge? because for verification i also plotted PCA for the 1000 genome values and the diagram was fine.
The PCA on plink 1.9 didn’t fail. It just gave empty results for the combined vcf file.
That’s a failure.
Ok. I will try to run it again with version 2.0