diff --git a/annotation/annotation_data/generate_annotation/gnomad_data.py b/annotation/annotation_data/generate_annotation/gnomad_data.py index 6ad4511ee..929f53105 100755 --- a/annotation/annotation_data/generate_annotation/gnomad_data.py +++ b/annotation/annotation_data/generate_annotation/gnomad_data.py @@ -17,21 +17,24 @@ GNOMAD_V_2_1 = "2.1.1" GNOMAD_V_3_1_2 = "3.1.2" GNOMAD_V_4_0 = "4.0" +GNOMAD_V_4_1_T2T_LIFTOVER = "4.1.t2t_liftover" GNOMAD_VERSIONS = { GNOMAD_V_2_1, GNOMAD_V_3_1_2, GNOMAD_V_4_0, + GNOMAD_V_4_1_T2T_LIFTOVER, } FILENAMES = { GNOMAD_V_2_1: "gnomad.%(capture_type)s.r2.1.1.sites.%(chrom)s.vcf.bgz", GNOMAD_V_3_1_2: "gnomad.%(capture_type)s.v3.1.2.sites.chr{chrom}.vcf.bgz", GNOMAD_V_4_0: "gnomad.%(capture_type)s.v4.0.sites.chr%(chrom)s.vcf.bgz", + GNOMAD_V_4_1_T2T_LIFTOVER: "gnomad.%(capture_type)s.v4.1.sites.GCA_009914755.4.trimmed_liftover.vcf.gz", } -GENOME_BUILDS = {"GRCh37", "GRCh38"} +GENOME_BUILDS = {"GRCh37", "GRCh38", "T2T-CHM13v2.0"} def get_infos_for_version(gnomad_version) -> tuple[list[str], list[str], list[str], list[str]]: # We deliberately leave out AF and "grpmax" stuff as we recalculate that later in 'calculate_allele_frequency' @@ -42,7 +45,7 @@ def get_infos_for_version(gnomad_version) -> tuple[list[str], list[str], list[st chr_x_male = ["AC_male", "AN_male", "AF_male"] chr_x_xy = ["AC_XY", "AN_XY", "AF_XY"] - if gnomad_version == GNOMAD_V_4_0: + if gnomad_version in (GNOMAD_V_4_0, GNOMAD_V_4_1_T2T_LIFTOVER): popmax_fields = grpmax_fields chr_x_male = chr_x_xy info_fields.extend(["faf95", "faf99", "fafmax_faf95_max", "fafmax_faf99_max"])