RELEASE-NOTES.org

ChangeLog v0.01 (2020/xx/xx) TBA

We are excited to announce the first GEMMA2LIB test release with new functionalities:

• [ ] Compute dominance
• [ ] Count missing genotypes at marker

IN PROGRESS

1. GEMMA1 pass through with ‘gemma2 gemma1 opts…’
   • [X] Pass through
2. GEMMA2 PLINK to GEMMA2/Rqtl2 format conversion
   • [X] Complete
3. GEMMA2 BIMBAM to GEMMA2/Rqtl2 conversion
   • [X] Convert GeneNetwork style BIMBAM (0,0.5,1) see https://github.com/rqtl/qtl2data/tree/master/BXD
   • [ ] Convert example mouse BIMBAM with 0.45 values, i.e., use real numbers
4. GEMMA2 GEMMA2/Rqtl2 to BIMBAM conversion
   • [X] Convert to BIMBAM as an intermediate solution
   • [X] Handle encoding of major/minor allele on the fly
5. Filtering
   • [X] Phenotypes (NA)
   • [X] other filters
6. Handle dominance
   • [ ] see genetics-statistics/GEMMA#34