2021-11-09 Meeting notes

Update requirements

@Yaw Nti-Addae

• Add crops stakeholders are more familiar with

  • Maize, Wheat

  • Small Intertek datasets

  • Load 2 datasets per crop

  • Extract across datasets

    • e.g. list of samples spanning multiple datasets

    • or, list of markers present in multiple datasets

  • GDM collapses markers, not dnaruns

• Benchmarks for new crops:

  • Extract by marker AND sample across datasets

  • Comment qualitatively on differences in output files

Cotton / potato

@Evan Rees

• Can remove Cotton - doesn’t add any new features

• Potato will be treated as qualitative

Plink format

@guilhem.sempere

• Add PLINK format for import / export comparison?

• Plain text, sample-oriented

• OR - rename Flapjack column to “sample-major” import

• PLINK

  • 4 plink formats

    • binary

  • 2 orientations

    • individual/sample

    • marker

sparse data

@guilhem.sempere

• Important to have a sparse dataset

  • sparse = high missingness

• @Yaw Nti-Addae will provide maize GBS dataset

• Should describe feature

Timeline

@Evan Rees

• Phase 1 platforms should have all comparisons finished by next meeting - early Dec

• Phase 2 benchmarks done by end of February