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changes.mady.by.user Yaw Nti-Addae

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changes.mady.by.user Evan Rees

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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

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