2.4 years ago
In the NHS diagnostic labs, the Genetic Technologists can sometimes report variants (up to and including targeted NGS panels) and collect evidence of the possible pathogenic status of the variant. This would mainly be trawling various databases (such as HGMD, dbSNP, OMIM, EXaC, Decipher) or using some online tools such as SIFT, Polyphen. Our NGS VCF files are annotated by Alamut Batch (although we have also used Annovar and other annotation sources such as Biomart), and the GTs use Alamut Visual / USCS genome browser to investigate the variants.
Possibly guidelines on the limitations of these databases / tools, something on the frequency of the variants in the various databases, maybe some information on constructing a family history and what genotypes you would be expecting. Something about compound Hets, CNVs (and how to find them, possible available tools like Conifer, ExomeDepth, XHMM etc, problems with using read depth when using amplicon based libraries), an idea of how a basic variant caller works, a rough guide on how the alignment against a reference genome works (just a general overview, you don't have to go into the guts of BWA MEM).
I should point out that most of the more complex reporting is done by the Clinical Scientists so many of the variants will already be characterised.
Overall more on the application of the tools rather than how to construct pipelines - which would be great but at what point do you stop?
Not sure how the French genetic labs are set up, but the UK labs are moving towards having dedicated Bioinformatics staff to set up the NGS analysis.