|
|
--- |
|
|
license: mit |
|
|
tags: |
|
|
- dna |
|
|
- variant-effect-prediction |
|
|
- biology |
|
|
- genomics |
|
|
--- |
|
|
# gnomAD variants |
|
|
For more information check out our [paper](https://www.nature.com/articles/s41587-024-02511-w) and [repository](https://github.com/songlab-cal/gpn). |
|
|
|
|
|
## Labels |
|
|
| Label | Meaning | |
|
|
| ----- | ---- | |
|
|
| True | Rare, singleton (AC=1) | |
|
|
| False | Common (MAF > 5%) | |
|
|
|
|
|
Note that the label does not indicate deleteriousness/pathogenicity. This is not suitable for a classification task. We recommend calculating enrichment or rare variants at the tail of model scores. |
|
|
|
|
|
## Usage |
|
|
* Pandas |
|
|
```python |
|
|
import pandas as pd |
|
|
df = pd.read_parquet("hf://datasets/songlab/gnomad/test.parquet") |
|
|
``` |
|
|
* Polars |
|
|
```python |
|
|
import polars as pl |
|
|
df = pl.read_parquet("https://huggingface.co/datasets/songlab/gnomad/resolve/main/test.parquet") |
|
|
``` |
|
|
* Datasets |
|
|
```python |
|
|
from datasets import load_dataset |
|
|
dataset = load_dataset("songlab/gnomad", split="test") |
|
|
``` |
