timflutre / PlantBreedGame

A serious game to teach plant selective breeding.
https://sourcesup.renater.fr/plantbreedgame/
GNU Affero General Public License v3.0
8 stars 2 forks source link

add `vcf.gz` genotype download #31

Closed juliendiot42 closed 8 months ago

juliendiot42 commented 8 months ago

This feature allow users to download the genetic data in a "vcf" format. It can be helpful if users want to import those data in external genetic tools.

However, VCF format request some information that we do not simulate (eg. REF / ALT), for those I use ..

For example:

##fileformat=VCFv4.3
##source="PlantBreedGame", data in this file are simulated.
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Coll0301    Coll0302
chr1    878 snp00007    .   .   .   PASS    .   GT  1/1 1/1 1/1 
chr1    1215    snp00009    .   .   .   PASS    .   GT  1/1 1/1 
chr1    3392    snp00020    .   .   .   PASS    .   GT  1/1 1/1 
chr1    6821    snp00029    .   .   .   PASS    .   GT  1/1 1/1 
chr1    8322    snp00032    .   .   .   PASS    .   GT  1/1 1/1 
timflutre commented 8 months ago

Thanks, it can indeed be useful.