Hi all, This project belong to a patient and I need some fast helps for the analysis
I have 2 WES samples from him, one of is Blood WES and another is cancer tissue WES. I just wanted to find germline mutation from Blood exome and also somatic mutation by comparing Blood and Cancer tissue samples, and finally finding relation among cancer genes with those mutations using annovar or other related tools.
First, I need to check my pipeline for blood (germline mutations):
After running Picard-MarkDuplicates I have ran BaseRecalibrator, PrintReads and HaplotypeCaller and VQSR and then running Annovar, Is it correct?
Second step finding somatic variations related to tumor tissue, what pipeline I should apply? ( I could not find exact pipeline from GATK website)
My third question is which tool I should used for find relation among variation and cancer related genes.
Thanks for your helps.
dear TriS thanks for your post, is was very constructive to me.