I'm quite new to this variant calling and analysis area. We have around 30 samples of RNAseq data of tumor and normal samples. I performed variant calling and obtained the multi-sample VCF file for all 30 samples. Now, my question is whether I can merge this RNAseq VCF to say a WGS 1000Genomes VCF (a subset of population) and do PCA analysis using Plink? Since RNAseq only contains certain regions such coding and non-coding RNAs and no intronic regions. Will it be logical to compare this with a WGS VCF which also includes introns? I actually tried this out and got a PCA plot, but I really want to make sure if this is correct?

Thanks, Vignesh