Cytogenetics - storing variants with uncertainty
- Dominant language
- Python
- Stars
- 30
- Forks
- 3
- Avg merge
- 9h 28m
- Merged PRs (30d)
- 42
Description
Cyto have a lot of data. It's currently stored in NxClinical in ISCN format
They use microarray probes that tile the genome, so data has inherit uncertainty - ie between these 2 probes, though sometimes they will export the data to be ISCNs w/o uncertainty, using say midpoint between 2 probes
If we could bring in cyto data, it would be useful for SA Path and Shariant. To do that, we would need to support uncertainty.
I uncertainty is a fundamental part of Variant, ie the same start/end but with different uncertainty is different.
```
outer_start = IntegerField(null=True)
outer_end = IntegerField(null=True)
```
You need to be able to store *no uncertainty* and *unknown* (ie ?), maybe magic numbers to avoid another boolean field, ie:
```
outer_start = null # no uncertainty (default in almost all cases)
outer_start = -1 # unknown
outer_start = 4231312 # the coordinate
```
Contributor guide
No contributing guide indexed for this repository
Assessment
This issue has not been assessed yet.