Small changes to wording.
#1
by
ozlemmuslu
- opened
README.md
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@@ -9,7 +9,7 @@ tags:
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- somatic-variant-calling
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---
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#
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This is an extra trees model for sensitive detection of somatic SNV candidates.
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@@ -85,7 +85,7 @@ scikit-learn GridSearchCV. Hyperparameters are given under the relevant section.
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#### Preprocessing
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Given
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1. BAM preprocessing (https://github.com/TRON-Bioinformatics/tronflow-bam-preprocessing)
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2. Candidate variant calling (https://github.com/TRON-Bioinformatics/tronflow-strelka2)
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3. Variant normalization and feature extraction (https://github.com/TRON-Bioinformatics/tronflow-vcf-postprocessing)
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#### Summary
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We observed high recall in both cross-validation and validation sets. Test set recall dropped slightly compared to control (0.8563 -> 0.8294), but precision increased.
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---
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## Environmental Impact
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Carbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).
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- **Hardware Type:** DGX2
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- **Hours used:** 2
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- **Compute Region:** Germany
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---
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- somatic-variant-calling
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---
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# Model Card for Model ID
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This is an extra trees model for sensitive detection of somatic SNV candidates.
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#### Preprocessing
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Given matched tumor-normal BAM files:
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1. BAM preprocessing (https://github.com/TRON-Bioinformatics/tronflow-bam-preprocessing)
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2. Candidate variant calling (https://github.com/TRON-Bioinformatics/tronflow-strelka2)
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3. Variant normalization and feature extraction (https://github.com/TRON-Bioinformatics/tronflow-vcf-postprocessing)
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#### Summary
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We observed high recall in both cross-validation and validation sets. Test set recall dropped slightly compared to control (0.8563 -> 0.8294), but precision increased.
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