Can we merge two VCF files

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

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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

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