Merge pull request #658 from broadinstitute/mw/mid_in_faf

Add mid to FAF and grpmax calcs
broadinstitute · Jan 24, 2024 · 89548e7 · 89548e7
2 parents 59bcfae + 2953763
commit 89548e7
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diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
@@ -227,7 +227,10 @@
 """
 
 POPS_STORED_AS_SUBPOPS = TGP_POPS + HGDP_POPS
-POPS_TO_REMOVE_FOR_POPMAX = {"asj", "fin", "oth", "ami", "mid", "remaining"}
+POPS_TO_REMOVE_FOR_POPMAX = {
+    "v3": {"asj", "fin", "mid", "oth", "ami", "remaining"},
+    "v4": {"asj", "fin", "oth", "ami", "remaining"},
+}
 """
 Populations that are removed before popmax calculations.
 """

diff --git a/gnomad/utils/vcf.py b/gnomad/utils/vcf.py
@@ -39,7 +39,10 @@
 Quality histograms used in VCF export.
 """
 
-FAF_POPS = ["afr", "amr", "eas", "nfe", "sas"]
+FAF_POPS = {
+    "v3": ["afr", "amr", "eas", "nfe", "sas"],
+    "v4": ["afr", "amr", "eas", "mid", "nfe", "sas"],
+}
 """
 Global populations that are included in filtering allele frequency (faf) calculations. Used in VCF export.
 """