nmdp-bioinformatics/grimm

Name: grimm

Owner: NMDP/Be The Match Bioinformatics Research

Description: GRIMM: Graph IMputation and Matching for HLA Genotypes

Created: 2018-02-14 16:50:11.0

Updated: 2018-02-14 17:19:59.0

Pushed: 2018-02-14 17:23:26.0

Homepage: null

Size: 12668

Language: Python

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README

GRIMM: Graph IMputation and Matching for HLA Genotypes

Graph-based imputation and matching

| Subdirectory | Description | | :————– | :———- | | graph_generator | Python code to generate (haplotype frequency) CSV files which can be imported into Neo4j | | gl_impute | Python code for graph-based imputation. | | multi_race_impute | Python code for graph-based imputation | | validation | Code for validation of components of this repository |

Walkthrough

1. Generate Initial Graph

Follow Graph Generation to generate haplotype frequency CSV files and import to Neo4j.

2. Perform Imputation

Follow Imputation directions to produce imputation results from frequency files.

3. Perform Matching

Follow Match Validation to perform matching and compare against consensus results.