RNA_feature¶

Purpose¶

Builds RNA-context features and annotations (ASE, hFDR, editing/imprinted/PON tags, sequence-context metrics).

Upstream¶

• genotyping

Required inputs¶

• germline_file
• ind_geno_filter_file
• error_count_file
• resources: gene_bed, dbsnp_vcf_file, imprinted_bed, editing_bed, PON_file, genome_fasta, reference_error_profile

Input interpretation¶

Input key	Source	Required	Interpretation
germline_file	genotyping output	Yes	Germline context used for RNA-level contrast and filtering logic.
ind_geno_filter_file	genotyping output	Yes	Candidate loci table entering RNA annotation and tests.
error_count_file	umi_combine output	Yes	Error-profile/count evidence used in RNA-context filtering features.
RNA/filter resources	resource_details.*	Yes	Annotation resources for dbSNP/editing/imprinted/PON/reference-error-derived features.

Parameters¶

From steps.RNA_feature:

• min_count_for_germline
• min_prior_for_germline
• default_range_of_gene
• p_threshold
• previous_base

Parameter interpretation highlights¶

Parameter	Interpretation
min_count_for_germline, min_prior_for_germline	Controls germline evidence sufficiency for RNA-context decisions.
default_range_of_gene	Window size for gene-context assignment when annotation ambiguity exists.
p_threshold	Main significance threshold for RNA-derived statistical tests.
previous_base	Sequence-context offset used in motif/context feature extraction.

Outputs¶

• RNA_feature: output_dir/RNA_feature/RNA_feature.txt
• parquet mirror: RNA_feature.parquet

Tuning notes¶

• This step merges several RNA-oriented annotation and statistical modules.
• Output fields are heavily used in final merged filtration rules.