Hi,
I have called variants from whole transcriptome sequencing data, following the "Calling variants in RNAseq" workflow that you recommended in the Methods and Algorithms webpage and using the following software versions: STAR 2.5.3a, PICARD 2.9.0, GATK 3.4. I had 4 samples corresponding to 2 related individuals, in replicate (technical replicates, i.e. different cell culture passage).
As a next step, I would like to compare the VCF files obtained from the 2 individuals, in order to identify common and specific variants.
Could you please suggest me how I should proceed? Also, what's the most appropriate way to merge the information obtained from the technical replicates?
Many thanks in advance,
Flavia