2021-10-19 Meeting notes

Date

Oct 19, 2021

Item	Notes

Item	Notes
Importing datasets	Distinguish between “unsupported” and “failed load” Imports and exports should be replicated 3x
Potato dataset / polyploid	Should we keep this? So small, may not be useful Should be kept - autopolyploid Alternate allele encoding Tricky with Hapmap need ad-hoc format to describe INDELs / polyploids Standardized in VCF Systems don’t necessarily maintain necessary data to encode a VCF metadata / header not kept MontyDB flattens polyploids in Hapmap output flattened `chr_1 100 A/A` `chr_1 100 A/C` `chr_1 100 A/G` single line `chr_1 100 A/A/C/G`
INDELs	Can INDELs be recoded as ‘i' and 'd’? Standard format +/- Hapmap doesn’t specify INDEL usage Problem: No standard separator is defined for hapmap Solution use `/` as separator for hapmap output sub-problem how does system resolve separator ambiguity? e.g. is `TTTT` `TT/TT` or `T/T/T/T`?
use cases	Simplify use cases Refine and flesh out Focus on compare / contrast Capture differences We DON’T want to create development work for anyone

@guilhem.sempere investigate how Gigwa resolves ambiguity in Hapmap format

@Evan Rees open discussion on slack WRT timelines

@Dave Matthews Fill out benchmarks for lettuce_chr1, lettuce_full, rice_full

@Dave Matthews Load potato and report any errors / irregularities

@guilhem.sempere Fill out benchmarks for lettuce_chr1, lettuce_full, rice_full

@guilhem.sempere Load potato and report any errors / irregularities

@Sebastian Raubach Fill out benchmarks for lettuce_chr1, lettuce_full, rice_full

@Sebastian Raubach Load potato and report any errors / irregularities