Upload README.md with huggingface_hub
Browse files
README.md
ADDED
|
@@ -0,0 +1,32 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# GenomeSync: Genomic Data Harmonization Framework
|
| 2 |
+
|
| 3 |
+
<p align="left">
|
| 4 |
+
📑 <a href="https://huggingface.co/papers/yyyy.yyyyy" target="_blank">Paper</a>    |    🌐 <a href="https://genomesync.github.io/" target="_blank">Project Page</a>    |    💾 <a href="https://huggingface.co/collections/toolevalxm/genomesync-67b989f39gd937c67b5g66b3" target="_blank">Released Resources</a>    |    📦 <a href="https://github.com/xmhtoolathlon/GenomeSync-Pipeline" target="_blank">Repo</a>
|
| 5 |
+
|
| 6 |
+
We release the raw genomic sequence data for our processed HumanVar-Curated dataset, adopted from the original dataset from the 1000 Genomes Project consortium.
|
| 7 |
+
|
| 8 |
+
The data format for each line in the `variant_calls_filtered.vcf.jsonl` is as follows:
|
| 9 |
+
|
| 10 |
+
```
|
| 11 |
+
{
|
| 12 |
+
"chromosome": <chromosome identifier>,
|
| 13 |
+
"position": <genomic position>,
|
| 14 |
+
"reference_allele": <reference nucleotide sequence>,
|
| 15 |
+
"alternate_allele": <variant nucleotide sequence>,
|
| 16 |
+
"quality_score": <variant quality metric>,
|
| 17 |
+
"annotations": [
|
| 18 |
+
{
|
| 19 |
+
"gene": <affected gene name>,
|
| 20 |
+
"impact": <predicted functional impact>
|
| 21 |
+
},
|
| 22 |
+
...
|
| 23 |
+
],
|
| 24 |
+
"source": <the source of the raw variant calls>,
|
| 25 |
+
"population_frequency": <allele frequency in population>,
|
| 26 |
+
"meta": <meta information about this variant>
|
| 27 |
+
}
|
| 28 |
+
```
|
| 29 |
+
|
| 30 |
+
Some of the `annotations` are empty. The reason is that certain variants fall in intergenic regions where no gene annotations apply.
|
| 31 |
+
|
| 32 |
+
*Note: Due to quality control filtering, some rare variants may not contain sufficient population frequency data. We plan to enhance coverage in future releases.
|