Versions Compared

Old Version 15

changes.mady.by.user Dave Matthews

Saved on

compared with

New Version 16

changes.mady.by.user Evan Rees

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

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 chromosome 1

hapmap

flapjack

hapmap

marker lists
Code Block
languagebash
cbsugobiizvm19:/
share
shared_data/test_data/lettuce/
  chr1/
    Lactuca__project1__2021-06-24__1152198variants__FLAPJACK.fjzip
cbsugobiizvm19:/share_data/test_data/lettuce/

    Lactuca__project1__2021-06-24__1152198variants__HAPMAP.zip
cbsugobiizvm19:/share_data/test_data/lettuce/markerlists

    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

...