References and annotation files for human germline analysis pipeline.

Similar to iGenomes but with Datalad and (somewhat) more up-to-date data. Follows the YODA principle for reproducible research.

Availabe datasets in GRCh38:

• Clinvar (VCF)
• CADD score
• dbSNP
• Reference genome
• VEP cache
• snpEFF cache

Disclaimer

• Dataset are not downloaded by default. Use datalad get to download them.
• Each dataset is its own git repository and has a license or a reference to it.
• Details about the version or type of database are stored in git log.
• Each major genome version is on a separate branch. Default branch is GRCh38. T2T support is coming soon.
• These are simply mirrors of publicly available data. That means
  • Dataset names are identical to the mirror, unless the name is not descriptive enough. For example, genome FASTA is named GCA_000001405.15_GRCh38_full_analysis_set.fna.gz. But clinvar is named clinvar_GCRh38.vcf.gz.
  • Some dataset must be decompressed manually