diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py index 75dde4a00..93633b5b1 100644 --- a/gnomad/resources/grch38/gnomad.py +++ b/gnomad/resources/grch38/gnomad.py @@ -221,7 +221,10 @@ """ 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 index 5842477d8..7d481351c 100644 --- 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. """