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Move gimbleprep away from textfile based inputs #19

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GertjanBisschop opened this issue Nov 20, 2023 · 2 comments
Open

Move gimbleprep away from textfile based inputs #19

GertjanBisschop opened this issue Nov 20, 2023 · 2 comments
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enhancement New feature or request
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1.0

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@GertjanBisschop
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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 GertjanBisschop added this to the 1.0 milestone Nov 20, 2023
@GertjanBisschop
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see for example #18

@GertjanBisschop GertjanBisschop added the enhancement New feature or request label Nov 20, 2023
@GertjanBisschop GertjanBisschop mentioned this issue Feb 6, 2024
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@GertjanBisschop
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see bio2zarr for a great library to parse a vcf and convert it to zarr.

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