indelPost

indelPost harmonizes representational ambiguities of small insertions and deletions (indels) in nucleotide sequences to derive correct complex indel alleles and improve variant effect annotation.

Key Features:

• Python implementation: Implemented as a Python library for programmatic integration into analysis workflows.
• Representational harmonization: Harmonizes ambiguous indel representations caused by different mapping algorithms, variant callers, and flanking sequence context.
• Realignment: Uses realignment to reconcile differing alignments that affect indel representation.
• Read-based phasing: Applies read-based phasing to resolve allele configurations for complex indels.
• Complex allele derivation: Derives correct complex indel alleles from simpler predictions produced by standard small variant detectors.
• Mapping and call-set reconciliation: Harmonizes discrepancies between different mappings and call sets to produce a unified indel representation.
• Annotation reliability: Improves the reliability of variant effect annotations by providing consistent allele representations.
• Comparative analysis support: Enables more robust comparative analyses across multiple data sources and callers.

Scientific Applications:

• Genetic disease research: Enables precise identification and characterization of indels relevant to genetic disease studies.
• Evolutionary studies: Facilitates accurate indel-based analyses in evolutionary and population genetics research.
• Personalized medicine: Improves indel interpretation for clinical and personalized medicine applications.
• Genomic data interpretation: Supports accurate interpretation of genomic datasets by reducing misannotation from inconsistent indel representations.

Methodology:

Harmonizes discrepancies between mappings and call sets via realignment and read-based phasing to derive correct complex indel alleles from simpler variant detector predictions.