merge_feature¶

Purpose¶

Merges RNA, spatial, read, and mappability feature tables into one integrated feature matrix and computes filtration tags.

Upstream¶

• spatial_feature
• mappability_feature
• read_feature
• RNA_feature

Required inputs¶

• RNA_feature
• spatial_feature
• read_feature
• mappability_feature

Input interpretation¶

Input key	Source step	Required	Interpretation
RNA_feature	RNA_feature	Yes	RNA-level annotation feature table.
spatial_feature / spatial_feature_results	spatial_feature	Yes	Spatial feature table or chunk manifest to be merged.
read_feature / read_feature_results	read_feature	Yes	Read-level feature table or chunk manifest to be merged.
mappability_feature	mappability_feature	Yes	Mappability/confounder feature table.
phasing_result	phasing	Recommended	Phasing summary that enriches merged features before filtration.
cluster_event_result	phasing	Recommended	Cluster-event flags used by filtration grouping (CLUSTER_EVENTS).

Parameters (steps.feature_filtration)¶

This step uses group-based filtration switches. If the section is omitted, the default enabled-group set in code is applied.

Group key	Interpretation
ASE	Filter loci flagged by allele-specific expression evidence.
hFDR	Filter loci with high hFDR-style artifact risk.
imprinted	Filter loci in imprinted-gene contexts.
homopolymer	Filter loci affected by homopolymer-related artifacts.
PON	Filter loci present in panel-of-normals evidence.
RNA_editing	Filter loci overlapping known RNA-editing contexts.
ABNORMAL_MISMATCHES	Filter loci with high/bias mismatch patterns.
LOW_READ_DIVERSITY	Filter loci with poor alternative-read diversity.
HIGH_MULTIPLE_MAPPIN	Filter loci with high multiple-mapping signal.
WIDE_DISTRIBUTION	Filter loci with broad suspicious mutant-probability distribution.
NEAR_READ_END	Filter loci dominated by near-read-end signal.
CLUSTER_EVENTS	Filter loci associated with cluster-like event patterns.
LOW_MAPQ	Filter low mapping-quality loci.
LOW_BASEQ	Filter low base-quality loci.

Tuning notes¶

• Start with defaults for production runs.
• Disable only specific groups when investigating why candidates were filtered.
• Document any filtration-group changes to preserve run comparability.

Outputs¶

• combine_feature: output_dir/all_feature.txt
• parquet mirror: output_dir/all_feature.parquet

Tuning notes¶

• Multi-index keys are #chrom, pos, ref, alt.
• Filtration summary is consolidated into the Filtration column (PASS or semicolon-separated tags).