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Update configure maf docstring #578

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merged 2 commits into from
Oct 2, 2024
Merged

Update configure maf docstring #578

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b68f90f
add to docstring about maf germline filtering
rxu17 Oct 1, 2024
a46e576
lint
rxu17 Oct 2, 2024
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9 changes: 9 additions & 0 deletions genie/database_to_staging.py
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Expand Up @@ -272,6 +272,15 @@ def get_whitelist_variants_idx(mafdf):
# TODO: Add to transform.py
def configure_maf(mafdf, remove_variants, flagged_variants):
"""Configures each maf dataframe, does germline filtering

Germline filtering for MAF files uses the gnomAD columns that refer to the
allele frequencies (AF) of variants in different population groups
from the gnomAD (Genome Aggregation Database). This filter will filter out
variants with a maximum AF > 0.05% across all populations which are typically
common germline variants.

Germline filtering for MAF files occurs during release instead of during processing
because the MAF file gets re-annotated during processing via genome nexus annotation.

Args:
mafdf: Maf dataframe
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