Move gimbleprep away from textfile based inputs

LohseLab / gimbleprep

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Move gimbleprep away from textfile based inputs #19

Open GertjanBisschop opened 10 months ago

GertjanBisschop commented 10 months ago

Ideally, gimbleprep would perform all required preprocessing steps on an array containing all variants. This can be done using sgkit. This is compatible with zarr. This would simplify the workflow a lot.

GertjanBisschop commented 10 months ago

see for example #18

GertjanBisschop commented 6 months ago

see bio2zarr for a great library to parse a vcf and convert it to zarr.