2021-06-24 Meeting notes

Owned by Evan Rees
Last updated: Jul 13, 2021
1 min read

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