资源简介：
---
license: mit
tags:
- dna
- variant-effect-prediction
- biology
- genomics
---
# gnomAD variants and GPN-MSA predictions
For more information check out our [paper](https://doi.org/10.1101/2023.10.10.561776) and [repository](https://github.com/songlab-cal/gpn).
## Querying specific variants or genes
- Install the latest [tabix](https://www.htslib.org/doc/tabix.html):
In your current conda environment (might be slow):
```bash
conda install -c bioconda -c conda-forge htslib=1.18
```
or in a new conda environment:
```bash
conda create -n tabix -c bioconda -c conda-forge htslib=1.18
conda activate tabix
```
- Query a specific region (e.g. BRCA1), from the remote file:
```bash
tabix https://huggingface.co/datasets/songlab/gnomad/resolve/main/scores.tsv.bgz 17:43,044,295-43,125,364
```
The output has the following columns:
| chrom | pos | ref | alt | GPN-MSA score |
and would start like this:
```tsv
17 43044304 T G -5.10
17 43044309 A G -3.27
17 43044315 T A -6.84
17 43044320 T C -6.19
17 43044322 G T -5.29
17 43044326 T G -3.22
17 43044342 T C -4.10
17 43044346 C T -2.06
17 43044351 C T -0.33
17 43044352 G A 2.05
```
- If you want to do many queries you might want to first download the files locally
```bash
wget https://huggingface.co/datasets/songlab/gnomad/resolve/main/scores.tsv.bgz
wget https://huggingface.co/datasets/songlab/gnomad/resolve/main/scores.tsv.bgz.tbi
```
and then score:
```bash
tabix scores.tsv.bgz 17:43,044,295-43,125,364
```
## Large-scale analysis
`test.parquet` contains coordinates, scores, plus allele frequency and consequences.
Download:
```
wget https://huggingface.co/datasets/songlab/gnomad/resolve/main/test.parquet
```
Load into a Pandas dataframe:
```python
df = pd.read_parquet("test.parquet")
```
---
许可证：MIT
标签：
- 脱氧核糖核酸(DNA)
- 变异效应预测
- 生物学
- 基因组学(Genomics)
---
# gnomAD 变异与GPN-MSA预测结果
如需了解更多详情，请参阅我们的[论文](https://doi.org/10.1101/2023.10.10.561776)与[代码仓库](https://github.com/songlab-cal/gpn)。
## 查询特定变异或基因
- 安装最新版[tabix](https://www.htslib.org/doc/tabix.html)：
在当前Conda环境中执行（可能速度较慢）：
bash
conda install -c bioconda -c conda-forge htslib=1.18
或新建独立Conda环境：
bash
conda create -n tabix -c bioconda -c conda-forge htslib=1.18
conda activate tabix
- 从远程文件查询特定区域（例如乳腺癌易感基因1(BRCA1)）：
bash
tabix https://huggingface.co/datasets/songlab/gnomad/resolve/main/scores.tsv.bgz 17:43,044,295-43,125,364
输出结果包含以下列：
| 染色体编号 | 位点 | 参考等位基因 | 变异等位基因 | GPN-MSA得分 |
示例输出如下：
tsv
17 43044304 T G -5.10
17 43044309 A G -3.27
17 43044315 T A -6.84
17 43044320 T C -6.19
17 43044322 G T -5.29
17 43044326 T G -3.22
17 43044342 T C -4.10
17 43044346 C T -2.06
17 43044351 C T -0.33
17 43044352 G A 2.05
- 若需执行多次查询，建议先将文件下载至本地：
bash
wget https://huggingface.co/datasets/songlab/gnomad/resolve/main/scores.tsv.bgz
wget https://huggingface.co/datasets/songlab/gnomad/resolve/main/scores.tsv.bgz.tbi
随后执行查询：
bash
tabix scores.tsv.bgz 17:43,044,295-43,125,364
## 大规模分析
`test.parquet`文件包含变异坐标、预测得分，以及等位基因频率与变异后果注释信息。
下载方式：
wget https://huggingface.co/datasets/songlab/gnomad/resolve/main/test.parquet
加载至Pandas数据框：
python
df = pd.read_parquet("test.parquet")
