Small changes to wording.

#1
by ozlemmuslu - opened
Files changed (1) hide show
  1. README.md +2 -14
README.md CHANGED
@@ -9,7 +9,7 @@ tags:
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  - somatic-variant-calling
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  ---
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- # extra_trees.snv
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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 a BAM file:
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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)
@@ -138,15 +138,3 @@ Sensitivity and precision, with sensitivity as the primary metric since the aim
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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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-
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- ## Environmental Impact
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-
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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.