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Add methylation resource for chrX #622

Merged
merged 5 commits into from
Oct 12, 2023
Merged

Add methylation resource for chrX #622

merged 5 commits into from
Oct 12, 2023

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klaricch
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@klaricch klaricch requested a review from jkgoodrich October 12, 2023 13:11
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I don't have write access, so I can't actually put those files at the specified paths

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jkgoodrich requested changes Oct 12, 2023
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If using gs://gnomad-public-requester-pays/ it will work while it's only located in that folder too, and then it will still work as expected when that file is removed and it's only in the gcp-public-data--gnomad bucket

gnomad/resources/grch38/reference_data.py Outdated
@@ -322,6 +322,15 @@ def _import_ensembl_interval(path) -> hl.Table:
},
)

# Methylation scores range from 0-12.
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Are these from the same (https://www.biorxiv.org/content/10.1101/2022.03.20.485034v2.full). or if not is there a comment we can add indicating where they came from?

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just checked - from the same source

gnomad/resources/grch38/reference_data.py Outdated Show resolved Hide resolved
gnomad/resources/grch38/reference_data.py Outdated Show resolved Hide resolved
klaricch and others added 3 commits October 12, 2023 11:13
@klaricch @jkgoodrich
Update gnomad/resources/grch38/reference_data.py
431be52 
Co-authored-by: jkgoodrich <33063077+jkgoodrich@users.noreply.github.com>
@klaricch @jkgoodrich
Update gnomad/resources/grch38/reference_data.py
0de0622 
Co-authored-by: jkgoodrich <33063077+jkgoodrich@users.noreply.github.com>
@klaricch
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23d105c
@klaricch klaricch requested a review from jkgoodrich October 12, 2023 15:26
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jkgoodrich approved these changes Oct 12, 2023
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lgtm

@klaricch klaricch merged commit 5bc67e4 into main Oct 12, 2023
@klaricch klaricch deleted the kl/x_methyl branch October 12, 2023 16:18
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