Model Card for Model ID
This is an extra trees model for sensitive 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 sensitive list of somatic small indels.
Direct Use
You can extract features from a matched tumor-normal sequencing pair using
https://github.com/TRON-Bioinformatics/tronflow-vcf-postprocessing and use this model on its output. Specific features this model utilizes are:
- primary_af
- primary_dp
- primary_ac
- primary_pu
- primary_pw
- primary_k
- primary_rsmq
- primary_rsmq_pv
- primary_rspos
- primary_rspos_pv
- normal_af
- normal_dp
- normal_ac
- normal_pu
- normal_pw
- normal_k
- normal_rsmq
- normal_rsmq_pv
- normal_rspos
- normal_rspos_pv
Downstream Use
This model is a part of VariantMedium somatic variant caller and is integrated directly into its workflow
https://github.com/TRON-Bioinformatics/VariantMedium.
Out-of-Scope Use
The model on its own is not intended to create a final list of variant calls, it is intended for filtering out noticeable false positives.
Bias, Risks, and Limitations
The model is trained on the output of cell line WES and an AML WGS, both originating from short read Illumina sequencing. It is tested for other cancer entities and 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
Training Procedure
scikit-learn GridSearchCV. Hyperparameters are given under the relevant section.
Preprocessing
Given matched tumor-normal BAM files:
- BAM preprocessing (https://github.com/TRON-Bioinformatics/tronflow-bam-preprocessing)
- Candidate variant calling (https://github.com/TRON-Bioinformatics/tronflow-strelka2)
- Variant normalization and feature extraction (https://github.com/TRON-Bioinformatics/tronflow-vcf-postprocessing)
Training Hyperparameters
1hyperparams = [
2 {
3 'n_estimators': [100, 200],
4 'max_depth': [5, 10],
5 'criterion': ['entropy'],
6 'max_features': ['sqrt', 'log2'],
7 'bootstrap': [True, False]
8 },
9 {
10 'n_estimators': [300, 400],
11 'max_depth': [10, 15],
12 'criterion': ['entropy'],
13 'max_features': ['sqrt', 'log2'],
14 'bootstrap': [True, False]
15 }
16]
17
Evaluation
Evaluation using CV and a left out cell line.
Testing Data, Factors & Metrics
Testing Data
Tested on independent data sets:
Metrics
Sensitivity and precision, with sensitivity as the primary metric since the aim was to filter out noticeable false positives instead of coming up with a final list of variants.
Results
| Metric | Test Set |
|---|
| Precision | 0.8564 |
| Recall | 0.6048 |
| F1 Score | 0.7089 |
Summary
Test set recall dropped slightly compared to control (0.6167 -> 0.6048), but precision increased (0.8216 -> 0.8564).
