Attendees
Evan Rees Yaw Nti-Addae Dave Matthews Moira Sheehan Sebastian Raubach guilhem.sempere Elizabeth Jones Former user (Deleted)
Systems to compare
1st round
Germinate
GDM
Gigwa
2nd round
MontyDB
GDR (if they respond)
BreedBase
Discussed benchmarking comparisons
Systems that don’t support VCF
Germinate
need alternate format for benchmarking
Suggest two tables
Systems that ignore metadata in VCF vs those that don’t
Only work with genotyping data itself hapmap format
Start with lettuce chromosome 1
if it works well across all systems, try other chromosomes
16 GB
Import time should include all processes pre- and post- import
Action items
- Generate Lettuce chromosome 1 hapmap and flapjack files (also whole genome as hapmap and flapjack) guilhem.sempere
- Reps will import Lettuce hapmap chromosome 1 (all)
- Define Lettuce chromosome 1 regions for benchmarking comparison guilhem.sempere
- Dave Matthews provide list of markers for extract. Done: cbsugobiizvm19:/share_data/test_data/lettuce/markerlists.zip
- Yaw Nti-Addae Look for tetraploid indel genome
- Evan Rees send meeting invite
Next meeting
July 13th, 12:00pm UTC