Model Card for Model ID
This is a 3D DenseNet model for detection of somatic indel candidates.
Model Details
Model Description
- Developed by: Özlem Muslu
- Funded by : European Research Council (“ERC Advanced Grant “SUMMIT” (Ugur Sahin): 789256”)
- License: cc-by-nc-nd-4.0
Model Sources
Uses
Using matched tumor-normal paired short read sequencing data, you can call a list of somatic small indels.
Downstream Use
This model is a part of VariantMedium somatic variant caller and is integrated directly into its workflow
https://github.com/TRON-Bioinformatics/VariantMediumOut-of-Scope Use
The model on its own is not intended to create a final list of variant calls, it is intended a part of a pipeline (
https://github.com/TRON-Bioinformatics/VariantMedium)
Bias, Risks, and Limitations
The model is trained on the output of cell line WES, TCGA WES, and an AML WGS, both originating from short read Illumina sequencing. It is tested for other cancer entities and mostly for solid tumors, but is not tested for non-Illumina sequencing.
Recommendations
We recommend using this model for Illumina-based WES and WGS (paired, short read).
Training Details
Training Data
Evaluation
Evaluation on two independent cohorts. More information can be found on our publication linked under:
https://github.com/TRON-Bioinformatics/VariantMediumTesting Data, Factors & Metrics
Testing Data
Tested on independent data sets:
