mappability_feature¶

Purpose¶

Annotates candidate loci with mappability information to flag low-uniqueness regions.

Upstream¶

• genotyping

Required inputs¶

• ind_geno_filter_mutation_list
• mappability_path

Input interpretation¶

Input key	Source	Required	Interpretation
ind_geno_filter_mutation_list	genotyping output	Yes	Candidate mutation list used for mappability lookup.
mappability_path	resource_details.mappability_path	Yes	Mappability track/resource used to annotate locus uniqueness.

Parameters¶

No major per-step thresholds are currently exposed; performance mainly scales with run.threads.

Parameter interpretation¶

Parameter area	Interpretation
run.threads / runtime parallel controls	Main performance knob for chromosome-group processing throughput.
mappability_path resolution	Most behavior is resource-driven; choice/version of mappability resource strongly affects output scores.

Outputs¶

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

Tuning notes¶

• Internally processed by chromosome groups.
• Output includes mappabilityScore used in final filtration logic.