
Dear all, 

although this question has been asked before (~ 2 years ago), if I may ask it again, as I am looking for some updated workflows, strategies, ideas :

"what would be the acceptable pipeline for processing WES or WGS data from primary tumors that do not have matched germlines sequences ?"

 many thanks, 

-- bogdan
MuTect and FreeBayes for SNVs are probably the most used tools for tumor-only analyses. Copy number, if you have some normals, you can try CNVkit, cn.mops (I think) and GATK4beta. If you need purity/ploidy and want to classify variants as germline vs somatic, there isn't much out yet, so we wrote our own tool PureCN (Bioconductor, try the much improved developer version if you like).  