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GenomeSync: Genomic Data Harmonization Framework
📑 Paper | 🌐 Project Page | 💾 Released Resources | 📦 Repo
We release the raw genomic sequence data for our processed HumanVar-Curated dataset, adopted from the original dataset from the 1000 Genomes Project consortium.
The data format for each line in the variant_calls_filtered.vcf.jsonl is as follows:
{
"chromosome": <chromosome identifier>,
"position": <genomic position>,
"reference_allele": <reference nucleotide sequence>,
"alternate_allele": <variant nucleotide sequence>,
"quality_score": <variant quality metric>,
"annotations": [
{
"gene": <affected gene name>,
"impact": <predicted functional impact>
},
...
],
"source": <the source of the raw variant calls>,
"population_frequency": <allele frequency in population>,
"meta": <meta information about this variant>
}
Some of the annotations are empty. The reason is that certain variants fall in intergenic regions where no gene annotations apply.
*Note: Due to quality control filtering, some rare variants may not contain sufficient population frequency data. We plan to enhance coverage in future releases.
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