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varfish-org / varfish-server

VarFish: comprehensive DNA variant analysis for diagnostics and research
MIT License
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Ingest Variants determined by Sanger Sequencing #578

Open your-highness opened 2 years ago

your-highness commented 2 years ago

Is your feature request related to a problem? Please describe. Many clinical relevant regions are difficult to sequence via NGS due to low complexity and homology (see #529). Usually, these diagnostics gaps are filled by PCR amplification and subsequent Sanger sequencing. This information is currently not uploaded to VarFish.

Describe the solution you'd like One could harness https://github.com/gear-genomics/indigo/blob/main/indigo.sh for automated SNV/InDel detection from raw sequencing traces (e.g. .abi files). Results can be saved as BCF/VCF. Most importantly, the import of these variants should be decoupled from NGS variant calls to assess variants correctly in downstream variant analysis.

Describe alternatives you've considered An alternative is to append Indigo calls to the NGS VCF. However, this approach does not trace the origin of the variant calls.

Additional context Honestly, the variant calling from Sanger sequencing requires alot of expert intervention and - despite the existence of reliable tools - most experiments have to be studied by experts visually as well. A linkout to an Sanger analysis program with the raw trace loaded would solve this problem.

holtgrewe commented 2 years ago

I had a quick look at indigo and clicked on "Example". Is the output of this suitable for interpretation by expert users already?

your-highness commented 2 years ago

I had a quick look at indigo and clicked on "Example". Is the output of this suitable for interpretation by expert users already?

Yes. A linkout to a Indigo server would be great to visualize Sanger sequencing results for expert assessment.

To seperate NGS from Sanger results one could seperately import Sanger results as TSV that will be marked by an INFO field that seperate NGS from Sanger calls.

BTW: Indigo is the web-server based on Tracy