Forum:Can we merge two VCF files – a RNAseq VCF and a Whole genome Sequencing (WGS) VCF to do PCA?
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?
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