My centre is working on an analysis pipeline for whole genome sequencing data. The sequencing and alignment are being performed off-site and my centre will be receiving VCF files for annotation and curation of variants.
There is little to no literature on validating pipelines for WGS. If anyone has any, would you kindly share?
Does anyone have a proposed pipeline for annotation? We will be using Alissa 5.3 Interpret and were thinking of initially filtering variants out by read depth and then sorting them into variant type (SNV, CNV, and SV). Or would it be better to have two separate pipelines for annotation? One for CNVs and one for SNVs?
Following the variant type filter for CNVs, would it then make sense to sort them by size (> or < 5kb)?
I was just hoping to bounce some ideas back and forth as this is a first for our centre and we currently do not have access to a bioinformatician.
Thank you for any and all help!