7/17/2019 Meeting notes Polyploid Working Group

 Andrzej – review experiences /  approaches with polyploids

Controls are G12 and H12 for DArT and Intertek can handle this

In cassavabase have an ordering form to create Intertek and DArT orders

DArT can provide a vcf as well as tab delimited

Have a script to convert vcf to genotyping files

In cassavabase will use vcf dosage data in GS ie user doesn't have to do anything

Have loaded 20,000 samples for DArT-LD already

Polyploids - can store dosage in cassavabase but not sure how to handle downstream tools

Elisa - can Guillaume share ontologies with potato base for molecular markers? Maybe have a follow up meeting on this? eg protocols, platform 

DArT-LD get 6-10,000 markers with good coverage - approx 20% missing data. Loading data as-is and imputing.

Dorcus - used DArT-seq for sweet potato. Ask for raw fastq files and use this for polyploid calling. Using a different vendor too optimized for polyploids. 

Jeff - need allele depth - need to communicate to DArT. Top on wish-list for Guillaume too. 

Dorcus - when call data with dosage the quality is not very high - need 3-4 times higher depth

For Yam just used the standard protocol

Jeff - have used intertek for KASP for potato - results were consistent with in-house results. For genome wide markers = have provided a set of SNPs for primer design 1,200-1,300 primers ordered. Waiting for wet-lab to see which will be working

Jeff - Dart wants the DNA of reference genome to set up for internal QC for development of plex. 

Guillaume - 100 bp sequence each side and they design sequence.

Correct and complete order form - will be generated by Sample Manager in future

Shipments of multiple of 16 x 96 plates. 

Agreed quality and quantity of sample

Agreed plasticware - Rajaguru would have this info and we can send it out 

Fixed plate layouts
Payment via Charge account

Agreed SNPs with VERY GOOD Assessment class (for KASP)