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Table of Contents

Genotyping data management systems

...

  • 8 CPUs

  • 64 GB RAM

  • 2 TB SSD

  • /storage mounted volumnvolume

  • /shared_data mounted volumnvolume

Users

Username

User

gadm

system

yaw

dave

francisco

...

Dataset

Format

Location

Maize NAM

CSV

/shared_data/test_data/NAM_HM32/csv

Simulated datasets

polyploid data in VCF

Moira share a dataset - invite to next meeting

indel data

rice high density array

vcf

The Rice High Density Array is : 700K SNPs x ~1500 samples

SNPs only

vcf too

Francisco loaded to Gigwa (own instance) already no problem

http://rs-bt-mccouch4.biotech.cornell.edu/staged_data/CSHL_EVA_Release_HDRA.tar

African rice

https://gigwa.ird.fr/gigwa/?module=AfricanRice

available as vcf

metadata availability?

3,000 rice genomes

too large? 29M SNPs

lettuce Wageningen

Public dataset

vcf

12M markers x 500 accessions

3 vcfs - one SNPs, one indels, one structural variants

40 GBs

https://www.nature.com/articles/s41588-021-00831-0/pub/CNSA/data2/CNP0000335/Other/variation
ftp.cngb.org/pub/CNSA/data2/CNP0000335/Other/variation

Lettuce

hapmap

flapjack

Code Block
languagebash
cbsugobiizvm19:
  /shared_data/test_data/genomics-systems-comparison/lettuce/
    chr1/
      Lactuca__project1__2021-06-24__1152198variants__FLAPJACK.fjzip
      Lactuca__project1__2021-06-24__1152198variants__HAPMAP.zip
      markerlists.zip
    full/
      Lactuca__project1__2021-06-28__12983735variants__FLAPJACK.fjzip
      Lactuca__project1__2021-06-28__12983735variants__HAPMAP.zip

Actions:

  •  presentations on polyploid data
  •  user accounts for participants
  •  identify benchmarking criteria

Benchmarking suggestions

Start with a SNP dataset - vcf ? - check with Sebastian and Breedbase (Titima)

Gigwa - 10s Ms markers x 1000s samples

Loading times?

Extract times - increasing marker and sample numbers?

Start with overview of features so we can understand better benchmarking

Action items April 29th

All - check can access site and load database - Gigwa still to be loaded to VM. Guilhem can access site but needs a user name

Yaw - update confluence so all participants can edit

Yaw - set up slack channel

Yaw - Have user accounts been set up? Set up and distribute. Need user names for people setting up databases.

Yaw - request VMs are not open for security

Dave to set up training with Liz to learn how to use GDM

Yaw make sure to invite Moira to next meeting to discuss polyploid data

Invite Breedbase to next meeting

Liz put together a table overview of features that we can all align against

...