2021-07-13 Meeting notes

Owned by Evan Rees, created
Last updated: Feb 09, 2022
1 min read

Date

Jul 13, 2021

Participants

  • @Evan Rees

  • @Dave Matthews

  • @Sebastian Raubach

  • @Mathieu Rouard

Goals

  • Decide on 2nd dataset

  • Decide on polyploid dataset

Discussion topics

Time

Item

Presenter

Notes

Time

Item

Presenter

Notes

 

rice high density array dataset

 

  • Could be moved to zvm19

  • VCF format, will be exported to flapjack



polyploid dataset



  • @Moira Sheehan had suggested Kiwi at prev meeting

  • @Yaw Nti-Addae was going to look for polyploid dataset w/ indels

 

lettuce dataset

 

  • Whole genome or one chromosome?

  • @Mathieu Rouard is there a bottleneck preventing us from loading whole genome datasets on certain platforms?

  • @Dave Matthews column 3 was '.' for all rows - no name for markers. Dave has constructed name from chrom + position.

  • @Evan Rees renamed markers in hapmap file - Lactuca__1152198variants__440individuals.renamed.hapmap

platform

VCF

hapmap

flapjack

platform

VCF

hapmap

flapjack

Gigwa

yes

yes

no

Germinate

no

no

yes

GDM

yes

yes

no

Action items

@Dave Matthews Load rice high density array dataset VCF to GDM and export as flapjack
@Dave Matthews Export lettuce chrom1 dataset to flapjack. 893 seconds
@Evan Rees rename shared folder and update paths
@Sebastian Raubach load lettuce chromosome 1 dataset
@Mathieu Rouard load lettuce chromosome 1 dataset
@Dave Matthews@Evan Rees load lettuce chromosome 1 dataset
@Dave Matthews download lettuce SNP VCF to zvm19 and split off chrom1
@Yaw Nti-Addae look for polyploid dataset (tetraploid w/ indels)
@Dave Matthews check marker names in zvm19:/shared_data/test_data/lettuce/chr1/Lactuca__1152198variants__440individuals.renamed.hapmap match those in VCF. They do; @Evan Reespleaserename markers in ../full/Lactuca__project1__2021-06-28__12983735variants__HAPMAP.zip too.
@Evan Rees schedule next meeting

Decisions