Variant calling

Variant calling is a common analysis strategy in e.g cancer related research. BCF can call somatic or germline variants on whole genome or exome data. We can also call variants on RNA. With respect to cancer, both tumor alone or tumor-normal pairs are commonly analysed.

In variant calling there are a several available analysis strategies available. At BCF, users often request the Sarek pipeline which is built upon a set of different variant callers that together call single nucleotide variants, insertions/deletions, copy number variations and so forth. For RNA, the GATK best practices is commonly applied. However, there are several analysis strategies available for variant calling and BCF has experience with several. 

Most of our users in cancer reserach prefer to have their variants annotated by e.g. PCGR (personal cancer genome report) for DNA where variants are organized into tiers of relevance to clinical significance. 

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