gafpack

A Rust tool to convert alignments from pangenome variation graphs into coverage maps, facilitating haplotype-based genotyping analysis.

Description

gafpack processes Graph Alignment Format (GAF) files against their corresponding Graph Fragment Assembly (GFA) graphs to generate coverage statistics. This is particularly useful for:

• Analyzing read coverage across pangenome variation graphs
• Supporting haplotype-based genotyping workflows
• Quantifying alignment distribution across graph nodes

Requirements

• Rust toolchain (cargo)
• Input files:
  • GFA format graph file
  • GAF format alignment file

Installation

Use cargo to build and install:

cargo install --force --path .

Usage

Basic usage requires a graph file (GFA) and alignment file (GAF):

gafpack -g graph.gfa -a alignments.gaf >coverage.tsv

Options

• -g, --graph: Input GFA pangenome graph file (required)
• -a, --alignments: Input GAF alignment file (required)
• -l, --len-scale: Scale coverage values by node length
• -c, --coverage-column: Output coverage vector in single column format
• -w, --weight-queries: Weight coverage by query group occurrences

Output Formats

1. Default (tabular):

   #sample        node.1  node.2  node.3  ...
   alignments.gaf 1.5     2.0     0.5     ...
   

2. Column format (-c flag):

   ##sample: alignments.gaf
   #coverage
   1.5
   2.0
   0.5
   ...
   

Examples

Scale coverage by node length:

gafpack -g graph.gfa -a reads.gaf --len-scale >scaled_coverage.tsv

Get column format output:

gafpack -g graph.gfa -a reads.gaf --coverage-column >coverage_vector.tsv