Our germline variant calling pipeline has been created in-house utilising Freebayes and the GATK rare variant discover workflow. We use this in combination with Ensembl's variant effect predictor (VEP) and gnomAD to filter for rare and predicted deleterious variants.
Following the sample QC, our somatic pipeline can be performed on tumor-normal matched samples. Samples are analysed using Sanger's variant pipelines for exome (cgpWXS) or whole-genome sequencing (cgpWGS) in addition our in-house pipeline that utlises Mutect2 and the GATK workflow tools.
We have developed quality control (QC) pipelines that automate a number of tools to ensure sample fidelity. This pipeline processes samples from RNA-seq and DNA-seq (exome and WGS) followed by mapping.