Genotype targeted variants
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
We should implement an analysis step for genotyping specific variants. For example, there are known variants in the ESR1, DPYD and PIK3CA genes that can affect treatment. The current variant calling analysis may catch some of the variants, but the filtering in that analysis is sometimes too hard and we may miss existing variants. A miss may also be due to low coverage on a specific location.
The analysis step should use one or more VCF files that specify the target variants as input. It should be possible to add more VCF files in the future. Genotyping can probably be done with HaplotypeCaller as we already do in the QC step. The results should be saved in VCF files attached to the Variant call raw bioassay. It is probably most practical to have one result VCF files for each target VCF file.
The result VCF files should be annotated in the same manner as the annotated VCF files from the existing variant calling analysis. This would make it possible to index and make the searchable by the Variant search extension.