Context
pyQTL currently excels at eQTL analysis, colocalization, and association plotting in human genetics. However, there is no Python library that handles classical biparental experimental cross QTL mapping (F2, backcross, RIL).
Feature request
Add modules or documentation for:
- Genotype encoding for biparental crosses (A/H/B or 0/1/2 with parent/F1 reference)
- Interval mapping / Haley-Knott regression for F2 populations
- Map-based narrowing (candidate interval identification by recombination)
- LOD calculation via likelihood ratio or linear model
- Permutation-based significance thresholds
- Input format conversion from common formats (JoinMap, QTL IciMapping, R/qtl2 cross2)
Use case
The Python ecosystem lacks a maintained, well-tested biparental QTL mapping library. Projects like ExcelMapBasedQTL (https://github.com/light-suzuki/Genotype) have to implement these algorithms from scratch or shell out to R/qtl2. Adding biparental support to pyQTL would fill a significant gap.
Why pyQTL
- Already has the right I/O infrastructure (BED, GCT, VCF)
- BSD-3 license is permissive for commercial/agricultural use
- Broad Institute backing ensures long-term maintenance
- Existing plotting and colocalization code complements biparental analysis well
Would the maintainers consider this direction?
Context
pyQTL currently excels at eQTL analysis, colocalization, and association plotting in human genetics. However, there is no Python library that handles classical biparental experimental cross QTL mapping (F2, backcross, RIL).
Feature request
Add modules or documentation for:
Use case
The Python ecosystem lacks a maintained, well-tested biparental QTL mapping library. Projects like ExcelMapBasedQTL (https://github.com/light-suzuki/Genotype) have to implement these algorithms from scratch or shell out to R/qtl2. Adding biparental support to pyQTL would fill a significant gap.
Why pyQTL
Would the maintainers consider this direction?