new module: updhmm

New local module proposal: updhmm (UPD detection from trio data)

Tool: updhmm
Purpose: Detection of Uniparental Disomy (UPD) from trio VCF data using a Hidden Markov Model

Background

Uniparental disomy (UPD) is a genetic condition where an individual inherits both copies of a chromosome (or chromosomal region) from one parent, rather than one copy from each parent. UPDhmm implements a Hidden Markov Model to detect UPD events through analysis of trio genotypes from sequencing data.

The model infers five hidden states:

• Normal biparental inheritance
• Father isodisomy
• Mother isodisomy
• Father heterodisomy
• Mother heterodisomy

Proposed Modules

This issue covers the addition of three interdependent submodules for UPD detection:

Module: updhmm/vcfcheck

Function: Validate and format trio VCF files for UPD analysis

Inputs: Trio VCF file
Outputs: Formatted VCF object with genotype encoding

Module: updhmm/calculateevents

Function: Calculate UPD events using Hidden Markov Model (Viterbi algorithm)

Inputs: Processed VCF from vcfcheck
Outputs: UPD event predictions (blocks)

Module: updhmm/collapseevents

Function: Collapse UPD events into consolidated regions

Inputs: UPD events from calculateevents
Outputs: Consolidated UPD regions

Rationale

These modules will enable the broader bioinformatics community to integrate UPD detection into Nextflow pipelines for trio sequencing analyses, particularly useful for:

• Clinical diagnostics
• Rare disease research

Additional Information

• Assignee: @saraamenasantamaria
• Reviewers: @saraamenasantamaria, @yocra3

Start by reviewing the UPDhmm repository and the three proposed entry points: updhmm/vcfcheck, updhmm/calculateevents, and updhmm/collapseevents. Confirm how trio VCF validation, Viterbi-based event prediction, and region consolidation should connect; done means all three interdependent modules support the described inputs and outputs for Nextflow integration.