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lines changed Original file line number Diff line number Diff line change @@ -273,6 +273,15 @@ def get_whitelist_variants_idx(mafdf):
273273def configure_maf (mafdf , remove_variants , flagged_variants ):
274274 """Configures each maf dataframe, does germline filtering
275275
276+ Germline filtering for MAF files uses the gnomAD columns that refer to the
277+ allele frequencies (AF) of variants in different population groups
278+ from the gnomAD (Genome Aggregation Database). This filter will filter out
279+ variants with a maximum AF > 0.05% across all populations which are typically
280+ common germline variants.
281+
282+ Germline filtering for MAF files occurs during release instead of during processing
283+ because the MAF file gets re-annotated during processing via genome nexus annotation.
284+
276285 Args:
277286 mafdf: Maf dataframe
278287 remove_variants: Variants to remove
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