# Data Sets

## Fusion Caller Output Files

### Set 1. chimeraviz example data

This dataset contains example fusion output from the [chimeraviz](https://bioconductor.org/packages/release/bioc/html/chimeraviz.html) BioConductor package.

Root directory: `/home/projects/hackseq17_3/datasets/chimeraviz_examples/`

Relevant files:

- `FusionMap_01_TestDataset_InputFastq.FusionReport.txt` - FusionMap output
- `PRADA.acc.fusion.fq.TAF.tsv` - PRADA output
- `defuse_833ke_results.filtered.tsv` - DeFuse output
- `ericscript_SRR1657556.results.total.tsv` - EricScript output
- `fusioncatcher_833ke_final-list-candidate-fusion-genes.txt` - FusionCatcher output
- `infusion_fusions.txt` - Infusion output
- `jaffa_results.csv` - JAFFA results
- `soapfuse_833ke_final.Fusion.specific.for.genes` - SOAPFuse results
- `star-fusion.fusion_candidates.final.abridged.txt` - STARfusion results

### Set 2. FusionCatcher example data

This data set contains a small FASTQ subset of files, containing reads supporting the fusions described [on the fusioncatcher github page](https://github.com/ndaniel/fusioncatcher/tree/master/test).

Root directory: `/home/projects/hackseq17_3/datasets/fusioncatcher_examples/`

Relevant files:

- `final-list_candidate-fusion-genes.txt` - fusioncatcher output
- `readme.txt` - README describing the detected fusions
- `reads_1.fq.gz` - Read 1 file
- `reads_2.fq.gz` - Read 2 file

### Set 3. AML Cell Line Data

This data set contains fusion results for three technical replicates from an AML cell line. 

Root directory: `/home/projects/hackseq17_3/datasets/aml_cell_line_examples/`

Under the root directory, you'll find directories named by tool and library. There are results for fusioncatcher, defuse, ericscript, STAR-fusion (with Oncofuse annotations),and PAVfinder.  

## Annotation Data Sources

### Tumor Fusion Gene Data Portal

- Located online at [PanCanFusV2](http://54.84.12.177/PanCanFusV2/)
- Downloaded to ORCA at `/home/projects/hackseq17_3/annotation_sources/tumour_fusion_gene_data_portal/`
- Contains 17,754 observations of 27 variables, in a format that is amenable to conversion to BEDPE
- Annotations include recurrence in TCGA tumour types, as well as additional manual and automated curations

### Database of Genomic Variants

- Located online at [DGV](http://dgv.tcag.ca/dgv/app/home)
- Latest release of GRCh37 dataset is on ORCA at `/home/projects/hackseq17_3/annotation_sources/dgv/`
- Contains 392,583 observations of 20 variables. These are mainly CNVs, insertions, and deletions though, so it seems it won't be as relevant here
- [Issue #14](https://github.com/rdocking/fusebench/issues/14)

### FusionCatcher Data Sources

- [Fusioncatcher](https://github.com/ndaniel/fusioncatcher) includes a whole lot of annotation resources 
- These are described in the [Fusioncatcher manual](https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md#23---genomic-databases)
- These mainly consist of just lists of Ensembl gene IDs
- Downloaded on ORCA at `/home/projects/hackseq17_3/tools/fusioncatcher_install/fusioncatcher/data/human_v89/`
- [Issue #21](https://github.com/rdocking/fusebench/issues/21)

### Atlas of Genetics and Cytogenetics in Oncology and Haematology

- [Atlas of Genetics and Cytogenetics in Oncology and Haematology](http://atlasgeneticsoncology.org/)
- Seems like there is no API or download access
- This database contains a lot of well-curated information - it may only be possible to query through the web interface though
- Depending on the eventual review interface, it may be possible to have links to this resource - it doesn't look like it's possible to include in an automated way though.

### CIViC

- [CIViC](https://civic.genome.wustl.edu/home) contains clinical interpretations of variants in cancer
- There is both API and bulk download access
- September 2017 release has been downloaded on ORCA at `/home/projects/hackseq17_3/annotation_sources/civic/`
- The contents of the individual files are described in [#13](https://github.com/rdocking/fusebench/issues/13)
- It looks like there ~85 annotated fusions

### ChimerDB

- [ChimerDB](http://203.255.191.229:8080/chimerdbv31/mindex.cdb)
- Contains three kinds of data:
    - "ChimerKB represents a knowledgebase including 1,066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences."
    - "ChimerPub includes 2,767 fusion genes obtained from text mining of PubMed abstracts."
    - "ChimerSeq module is designed to archive the fusion candidates from deep sequencing data."
- These data files are available as MySQL and Excel-formatted dump files
- These aren't downloaded to ORCA yet

### TICdb

- [TICdb](http://www.unav.es/genetica/TICdb/)
- 1,374 annotated fusions, with annotations of the gene partners and actual fusion sequence, with links to Pubmed or Genbank
- Not downloaded to ORCA yet

### ChiTaRS

- [ChiTaRS](http://chitars.bioinfo.cnio.es/)
- 20,754 annotations for humans, downloaded from `http://chitars.bioinfo.cnio.es/downloads.html`
- Downloaded to ORCA at: `/home/projects/hackseq17_3/annotation_sources/chitars/all_human_ChiTaRS_coord.csv`
- Note that it looks like this data source hasn't been updated since late-2014

### COSMIC

- [Catalogue of Somatic Mutations in Cancer](http://cancer.sanger.ac.uk/cosmic)
- [Cell Lines Project](http://cancer.sanger.ac.uk/cell_lines)
- There is an API for querying COSMIC, and bulk downloads are available at [downloads](http://cancer.sanger.ac.uk/cosmic/download)
- The downloads are via SFTP - `@rdocking` has credentials but hasn't downloaded things to ORCA yet
- See also [#29](https://github.com/rdocking/fusebench/issues/29)