System features

Extract data by marker list

N

Y

Y

Extract data by sample list

Y

Y

Y

Y

Extract data by chromosome

Y

N

Y

Y

Extract data by position (single point, range?) on chromosome

Y

N

Y

Y

Extract data following by variant type (eg indel/SNP etc?)

Y

N

Y

Y

Extract data by data type (SNPs, dominant, codominant, SSR etc)

can we clarify the difference with the one just above?

Y

Y

Extract data following filtering by functional annotations eg?

Y

N

Y

N

Extract data following filtering by genotyping patterns eg?

Y

?

?

?

Extract data with multiple groups of samples (extract data by a sample group/list?)

Y

Y

?

Y

Extract data following filtering by metadata eg

Y

N

Y

Visualizing genotypes as strings

Y

In downstream Flapjack application

Y

In downstream Flapjack application

Visualizing genotypes through graphical representation

Y

In downstream Flapjack application

Y

Map histogram

import format plink

Y

N

?

import format flapjack

N

Y

Y

Import format vcf

Y

Y

N

Import format hapmap

Y

Y

Y

Import format csv or txt

soon?

Y

Y

Export format hapmap

Y

Y

Y

Y

Export format Flapjack

Y

Y

Y

Y

Support for indels

Y

soon!

Y

N

Support for polyploids

Y

Y

?

Y/N

Support for mixed-length polyploids eg triploids and tetraploids in the same file

can we have an example file?

N

N

Y/N

Support for phasing

Y

Y

?

N

Support for marker metadata

Y

Y

?

Basic

Support for sample metadata

Y

Y

?

Y

Interoperability: standard API support (as a data-provider)

Y

Y

Y

Y

Interoperability: standard API support (as a data-consumer)

Y

Y

N

Y

Interoperability: Supports feeding genotypes through API

Y

Y

N

Y

Interoperability: supports BrAPI

Y

Y

maybe-WIP

Y

Interoperability: Link to external software (e.g. Jbrowse)

Y

N

N

Software availability: distributable

Y

Y (but hard)

Y

Software availability: open-source

Y

Y

Y

Software availability: available as a Docker container

Y

Y

WIP

Y

Software availability: embeddable

Y

?

?

?

Data is compact (percentage of disk space occupied by the data once in the system, compared to that occupied by the original VFC file)

Y

Y?

?

Y?

Integrated with downstream molecular breeding tools

Could we consider rephrasing "Integrated with downstream molecular breeding tools" to "Scientific fields of application"? As a more open question, we think this would leave more space for everyone to be able to specify something.

Y

?

?