gafpack

Calculate node coverage from GAF alignments to GFA variation graphs.

This is useful for:

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

Install

Install using:

cargo install --git https://github.com/pangenome/gafpack

Or build from source:

git clone https://github.com/pangenome/gafpack
cd gafpack
cargo build --release

Usage

Basic usage:

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

The GFA file can be gzip/bgzip compressed (.gz or .bgz).

Options

• --gfa: Input GFA graph file (required)
• -g, --gaf: Input GAF alignment file (required)
• -l, --len-scale: Scale coverage by node length
• -c, --coverage-column: Output coverage vector as single column
• -w, --weight-queries: Weight coverage by query occurrences

Output Formats

Default (tabular):

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

Column format (with -c, --coverage-column):

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