songlab/deprecated-full-gnomad

---
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")
```

原始信息汇总

gnomAD variants and GPN-MSA predictions

数据集概述

该数据集包含gnomAD变异数据及其GPN-MSA预测结果。

数据查询

安装tabix

• 在当前conda环境中安装： bash conda install -c bioconda -c conda-forge htslib=1.18

• 在新conda环境中安装： bash conda create -n tabix -c bioconda -c conda-forge htslib=1.18 conda activate tabix

查询特定区域

• 远程查询特定区域（例如BRCA1）： bash tabix https://huggingface.co/datasets/songlab/gnomad/resolve/main/scores.tsv.bgz 17:43,044,295-43,125,364

  输出包含以下列： | chrom | pos | ref | alt | GPN-MSA score | 示例输出： 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

本地查询

• 下载文件到本地： 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

• 本地查询特定区域： bash tabix scores.tsv.bgz 17:43,044,295-43,125,364

大规模分析

test.parquet文件包含坐标、评分、等位基因频率和后果。

• 下载文件： bash wget https://huggingface.co/datasets/songlab/gnomad/resolve/main/test.parquet

• 加载到Pandas数据框： python df = pd.read_parquet("test.parquet")