manual_review_classifier

A walk-through of the manual_review_classifier repo can be found on the Wiki page.

Table of Contents

0. Chapter 1 - Background Information
1. Authors
2. Citation
3. About
4. Installation
1. Chapter 2 - Identification of Somatic Variants in Sequencing Data
1. Automated Somatic Variant Calling
2. Somatic Variant Refinement (SVR)
2. Chapter 3 - Methods and Analysis for Machine Learning Models
1. Data Assembly
2. Logistic Regression Model
3. Random Forest Model
4. Deep Learning Model/li>
5. Model Evaluation
6. Inter-reviewer Variability
7. Orthogonal Validation
8. Re-review Analysis
3. Chapter 4 - Using DeepSVR (Deep Learning Model)
1. Create the Classifier/li>
2. Prepare Your Data
3. Classify Your Data

Installation of manual_review_classifier repo

Install the package using the editable (-e option) mode for ease in development

git clone [manual_review_classifier_link]

cd manual_review_classifier

pip install -e .

Test instalation

prepare_manual_review_classifier_data -h

Test

To run tests Download GRCH37 fasta and fasta index file to home directory as '~/grch37.fa' and '~/grch37.fa.fai'