Skip to content

Update some gnomAD resources from lists to version dictionaries #522

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Mar 28, 2023
Merged

Update some gnomAD resources from lists to version dictionaries #522

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
73ac308
Update freq resources to version dictionaries
mike-w-wilson Mar 27, 2023
9bc5a1a
Change hyphens to underscores in subsets
mike-w-wilson Mar 28, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
117 changes: 76 additions & 41 deletions gnomad/resources/grch38/gnomad.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,17 +19,20 @@
DATA_TYPES = ["genomes"]

GENOME_POPS = ["AFR", "AMI", "AMR", "ASJ", "EAS", "FIN", "NFE", "SAS", "OTH"]
SUBSETS = [
"non_v2",
"non_topmed",
"non_cancer",
"controls_and_biobanks",
"non_neuro",
"tgp",
"hgdp",
]
SUBSETS = {
"v3": [
"non_v2",
"non_topmed",
"non_cancer",
"controls_and_biobanks",
"non_neuro",
"tgp",
"hgdp",
],
"v4": ["ukb", "non_ukb", "non_topmed"],
}
"""
Order to sort subgroupings during VCF export.
Order to sort subgroupings during VCF export by version.

Ensures that INFO labels in VCF are in desired order (e.g., tgp_raw_AC_esn_XX).
"""
Expand All @@ -48,9 +51,21 @@
Used to stratify frequency annotations (AC, AN, AF) for each sex.
"""

POPS = ["afr", "ami", "amr", "asj", "eas", "fin", "nfe", "oth", "sas", "mid"]
POPS = {
"v3": ["afr", "ami", "amr", "asj", "eas", "fin", "nfe", "oth", "sas", "mid"],
"v4": [
"afr",
"amr",
"asj",
"eas",
"fin",
"mid",
"remaining",
"sas",
],
}
"""
Global populations in gnomAD v3.
Global ancestry groups in gnomAD by version.
"""

COHORTS_WITH_POP_STORED_AS_SUBPOP = ["tgp", "hgdp"]
Expand Down Expand Up @@ -186,36 +201,56 @@
Populations that are removed before popmax calculations.
"""

DOWNSAMPLINGS = [
10,
20,
50,
100,
200,
500,
1000,
2000,
5000,
10000,
15000,
20000,
25000,
30000,
40000,
50000,
60000,
70000,
75000,
80000,
85000,
90000,
95000,
100000,
110000,
120000,
]
DOWNSAMPLINGS = {
"v3": [
10,
20,
50,
100,
200,
500,
1000,
2000,
5000,
10000,
15000,
20000,
25000,
30000,
40000,
50000,
60000,
70000,
75000,
80000,
85000,
90000,
95000,
100000,
110000,
120000,
],
"v4": [
10,
100,
1000,
2000,
5000,
10000,
15000,
20000,
25000,
50000,
100000,
150000,
200000,
300000,
400000,
500000,
],
}
"""
List of the downsampling numbers to use for frequency calculations.
List of the downsampling numbers to use for frequency calculations by version.
"""

gnomad_syndip = VersionedMatrixTableResource(
Expand Down