Gene Burden Module

Statistical methods for gene burden analysis

Gene burden analysis module (CMC/CAST collapsing test for rare variant association).

Supports ‘samples’ (binary collapse) and ‘alleles’ (max dosage collapse) modes with Fisher’s exact test and multiple testing correction (FDR/Bonferroni).

variantcentrifuge.gene_burden.drop_transcript_duplicates(df)

Keep one row per variant per gene before burden/association tests.

--split-snpeff-lines writes one row per transcript, so a variant on two transcripts of a gene would enter the genotype matrix twice. snpEff orders annotations by severity, so the first row kept is the most severe consequence.

Parameters:

df (DataFrame)

Return type:

DataFrame

variantcentrifuge.gene_burden.perform_gene_burden_analysis(df, cfg, case_samples=None, control_samples=None, vcf_samples=None)

Perform gene burden analysis using collapsing (CMC/CAST) with Fisher’s exact test.

Supports column-based, packed GT, and legacy per-variant count aggregation.

Parameters:

• df (DataFrame)

• cfg (dict[str, Any])

• case_samples (set[str] | None)

• control_samples (set[str] | None)

• vcf_samples (list[str] | None)

Return type:

DataFrame