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Update configure maf docstring (#578)
* add to docstring about maf germline filtering * lint
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genie/database_to_staging.py

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@@ -273,6 +273,15 @@ def get_whitelist_variants_idx(mafdf):
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def configure_maf(mafdf, remove_variants, flagged_variants):
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"""Configures each maf dataframe, does germline filtering
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Germline filtering for MAF files uses the gnomAD columns that refer to the
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allele frequencies (AF) of variants in different population groups
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from the gnomAD (Genome Aggregation Database). This filter will filter out
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variants with a maximum AF > 0.05% across all populations which are typically
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common germline variants.
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Germline filtering for MAF files occurs during release instead of during processing
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because the MAF file gets re-annotated during processing via genome nexus annotation.
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Args:
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mafdf: Maf dataframe
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remove_variants: Variants to remove

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