2022-02-08 Meeting notes

 Date

Feb 8, 2022

 Participants

  • @Evan Rees

  • @Dave Matthews

  • @Francisco Agosto

  • @Mathieu Rouard

  • @guilhem.sempere

  • @Moira Sheehan

  • @Pierre Larmande

  • @Sebastian Raubach

 Goals

  •  

 Discussion topics

Item

Presenter

Notes

Item

Presenter

Notes

PLINK format

@guilhem.sempere

  • Should we keep PLINK?

  • Keep for now - pending phase 2 systems

sparse datasets

@guilhem.sempere @Evan Rees

Use maize_chr1 (50%)

extraction across datasets

@Evan Rees

load all 10 maize chromosomes

only need to benchmark chromosome 1

 

extraction by sample will be across datasets

 

storing outputs

@Evan Rees

Save extracted files to /shared_data/test_data/genomics-systems-comparison/output/{system}/{format}

completion plan

@Evan Rees

Aim to have all benchmarks filled in by next meeting Mar 8, 2022

 Action items

@Evan Rees contact Breedbase
@Mathieu Rouard contact PostgreSQL Tripal folks about potential inclusion
@guilhem.sempere provide maize_chr1 as Flapjack and VCF for others to benchmark

 Decisions