Can we merge two VCF files - a RNAseq VCF and a Whole genome Sequencing (WGS) VCF to do PCA?
Entering edit mode
8 weeks ago
Vignesh • 0

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

PCA Whole-genome-sequencing RNAseq VCF Plink • 181 views

Login before adding your answer.

Traffic: 1518 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6