This repository hosts ressources for human germline analysis : reference genome and databases for variants annotation. This is intented to use with Ensembl [https://www.ensembl.org/info/docs/tools/vep/index.html](Variant Effect Predictor) or VEP.

Ressources, called assets, are managed with scidataflow for download, update and integrity checks.

Available data

Asset	Latest	Other
Genome	GRCh38.p14 (md5sum)	GRch38 + index (md5sum)
CADD	v1.7 on GRCh38 (md5sum)
Clinvar	GRCh38
dbSNP	GRCh38.p14 (md5sum)
VEP	v112 on GRCH38 (sum)

Notes:

• Only latest versions for each dataset are available at the moment.
• Only public ressources through https are used.
• Data is roughly 140G in size
• Genome is available as "pipeline-ready" (GRCh38) or latest version without indexes (GRCh38.p14)

Filename convention

Filename are lowercase only and renamed to match $DB_$GENOME_$VERSION_$DESC.$EXT with

• DB is the database name (e.g clinvar),
• GENOME is grch38 or t2t
• VERSION is the database version (v1.7 for clinvar for exaple)
• DESC is a description (snv for example)
• EXT is the file extension (often .gz) If there are different versions of the database, all versions are stored in the same folder $DB.