# GWASAdapter
Auto-generated config schema for the current JBrowse release — see the
[config guide](https://jbrowse.org/jb2-staging/docs/config_guide) for concepts. Provided by the `gwas` plugin.
[View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/gwas/src/GWASAdapter/configSchema.ts).
## Example usage
```js
{
type: 'GWASTrack',
trackId: 'my_track',
name: 'My track',
assemblyNames: ['hg38'],
adapter: {
type: 'GWASAdapter',
uri: 'https://example.com/summary_stats.txt.gz',
},
}
```
`summary_stats.txt.gz` infers `GWASAdapter` and `GWASTrack` on its own, and
`name` defaults to the file name. In a config declaring one assembly,
`assemblyNames` comes from there too — see
[the shortest track](https://jbrowse.org/jb2-staging/docs/config_guides/tracks#the-shortest-track).
```js
{
trackId: 'my_track',
uri: 'https://example.com/summary_stats.txt.gz',
assemblyNames: ['hg38'],
}
```
Reading a raw p-value column instead, transformed to -log10(p) at load:
```js
{
type: 'GWASTrack',
trackId: 'my_track',
name: 'My track',
assemblyNames: ['hg38'],
adapter: {
type: 'GWASAdapter',
uri: 'https://example.com/summary_stats.txt.gz',
scoreColumn: 'pval',
scoreTransform: 'negLog10',
},
}
```
_See the **Config slots** section below for all available configuration fields._
adapter for GWAS results files; a BedTabixAdapter with `scoreColumn` defaulted
to `neg_log_pvalue` so files load with a sensible Manhattan plot score out of
the box
## Related links
- **Track:** [GWASTrack](../gwastrack)
- **Display:** [LinearManhattanDisplay](../linearmanhattandisplay)
- **Base config:** [BedTabixAdapter](../bedtabixadapter)
## Config slots
These slots go inside the track's `adapter`:
`"adapter": { "type": "GWASAdapter", ... }`. It also accepts the
[shorthand](https://jbrowse.org/jb2-staging/docs/config_guides/file_types#the-uri-shorthand) keys `uri`,
`baseUri`, `csi` in place of writing a location slot out. Slot types
(`fileLocation`, `frozen`, ...) are explained in the
[config slot types reference](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types). Slots a base
configuration contributes are listed here too, so this table is the whole
surface.
| Slot | Description |
| --- | --- |
| **scoreColumn**
[`string`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#string) = 'neg_log_pvalue' | BED column to read as the Manhattan plot score |
| **scoreTransform**
[`string`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#string) = 'none' | transform applied to `scoreColumn` to produce the Manhattan -log10(p) value: `none` (column is already -log10, e.g. Pan-UKBB neglog10_pval_*), `negLog10` (column is a raw p-value), `negLog10FromLn` (column is a natural-log p-value, e.g. Pan-UKBB Hail `ln P`), or a `jexl:...` expression of `score` for anything else (e.g. `jexl:-log10(score)`) — arbitrary but slower than the native modes, so opt-in only |
| **ldAdapter**
[`frozen`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#frozen) = null | optional PLINK .ld sub-adapter (PlinkLDAdapter / PlinkLDTabixAdapter) supplying pairwise r² used for LocusZoom-style coloring when the Manhattan display's `colorBy` is `ld`; null disables it |
| Inherited from [BedTabixAdapter](../bedtabixadapter) | 6 slots |
| **bedGzLocation**
[`fileLocation`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#filelocation) = { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' } | location of the bgzip-compressed BED, sorted by position. Must be bgzip rather than plain gzip, which tabix cannot index. |
| **columnNames**
`stringArray` = [] | List of column names. A column named like a standard BED column is parsed as that column's type (chromStart numeric, blockSizes a numeric list); any other column is text |
| **autoSql**
[`string`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#string) = '' | The autoSql definition for the data fields in the file |
| **disableGeneHeuristic**
[`boolean`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#boolean) = false | Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications) |
| **index.indexType**
[`stringEnum`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#stringenum) (TBI, CSI) = 'TBI' | `TBI` is the usual `tabix` output. `CSI` is required for a reference longer than 512 Mb, which TBI cannot address. |
| **index.location**
[`fileLocation`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#filelocation) = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' } | location of the tabix index. Only needed when it is not named `.tbi` (or `.csi`), which is what the `uri` shorthand assumes. |