Genomic data sources¶
Legend
somatic
cancer
cancer analysis germline
germline
rare disease
rare disease analysis germline
Primary delivery (single sample only)¶
All files can be found in the /genomes/by_date folder. You can find paths to specific files using the Labkey table genome_file_types_and_paths and filtering by the file_type and/or file_sub_type.
| 100kGP NSv2 (Illumina) | 100kGP NSv4 (Illumina + GEL) | 100kGP DRAGEN (GEL realigned cancer programme) | NHS GMS DRAGEN (GEL) | ||
|---|---|---|---|---|---|
| Reference genome | GRCh37 | GRCh38 (Decoy, no alt) | GRCh38 (DeAlt_HLA) | GRCh38 (DeAlt_HLA) | |
| Alignment | Aligner | ISAAC | ISAAC | DRAGEN 3.2.22 | DRAGEN 3.2.22 |
| BAM | |||||
| CRAM | |||||
| Small variants | germline VCF | ||||
| somatic VCF | |||||
| gVCF (germline) | |||||
| Structural and Copy Number Variation | SV VCFs | ||||
| CNV VCFs | |||||
| SV and CNV in a single VCF |
Supporting genomic files (i.e. annotated or multi-sample)¶
All files can be found in the /gel_data_resources folder.
| 100kGP NSv2 (Illumina) | 100kGP NSv4 (Illumina + GEL) | 100kGP DRAGEN (GEL realigned cancer programme) | NHS GMS DRAGEN (GEL) | ||
|---|---|---|---|---|---|
| Joint-called VCFs | joint-called VCF1 | ||||
| joint-called gVCF1 | |||||
| SV diploid (joint-called) | |||||
| Cancer interpretation related | cancer small variants annotated | ||||
| germline small variants VCF | |||||
| somatic small variants VCF (cancer programme) |