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Date

Participants

Discussion topics

Time

Item

Presenter

Notes

· New public Confluence site allowing easier access for everyone https://gobiiproject.atlassian.net/wiki/x/A4AKB

Liz


· Slack channel now created


Liz


Review meeting agenda CIP May https://gobiiproject.atlassian.net/wiki/x/IgEIB

Tour of genebank facilities Friday?

Marcello

Carpentries Lindsay - Dorcus send out an email for interest. Need R and R studio set up - Lindsay will send out specifications

Umesh and Marcello and Trushar can help,

Liz talk earlier - Friday and then Lindsay

Get a number count for the genebank tour closer to the time - Friday afternoon is good

Need for vcf filtering tools - Lindsay and Marcelo can cover

Lindsay recommends an R package - VariantAnnotation (Bioconductor)

Read depth - how this affects calling dosage? sweet potato need 100X - Jeff’s talk will cover this and Lindsay will too

Small numbers of markers - eg amplicon technologies , KASP dosage for potato - Petra says can do now - Eng present on technologies for polyploids.

Luis has genotyped with the fluidigm system with Cassava - converted Illumina markers. 50/50 dosage

Review crop specialist needs – crop contacts https://gobiiproject.atlassian.net/wiki/x/KQEIB

Dorcus

Local arrangements

Recordings

Dorcus

Would be good to get recordings and can post them on the EiB website

Visa requirements for Americans?

Jeff

None - Dorcus will check - no, none needed

Dataset sharing site

Liz

Github?

Marcelo - Mapping section have a vcf F1 population with 2 hexaploid parents

Can also be used for haplotyping - Umesh will present haplotyping in populations

Dorcus have any tetraploid F1 datasets? No but have a GWAS panel

Marcelo has public datasets for F1 tetraploids

Linsday may use a different dataset for GWAS

Key datasets

Mapping - F1 triploids (Trushar), tetraploid (SolCAP) and hexaploid (Marcelo)

GWAS - diversity population - tetraploid (Umesh has) and hexaploid (Dorcus has raw data)

Data types: vcf, Illumina chips (banana)

Action items

  •  Dorcus Gemenet to get technical support to do video recordings on Day 1 and 2
  •  Elizabeth Jones to send Dorcus info on ppt Friday
  •  Lindsay Clark to send Dorcus info on what is required (laptop set up, minimum skills) for attendees for Carpentries session Friday
  •  Dorcus Gemenet to send out Friday open-session details to relevant CIP teams and see who is interested. For approx 25 people?

  •  Marcelo Mollinari to send out Github link so people can post datasets there
  •  Marcelo Mollinari to discuss with team whether we need extra time for variant calling pipelines and vcf filtering tools - lots of interest from the group. If we do this Friday we may not have time for Carpentries session

Decisions