cosigt

cosigt is a tool for genotyping complex loci in pangenome graphs. It takes as input a path coverage matrix for a locus from a pangenome graph (generated with odgi paths) and read alignments to the graph locus for a sample (converted to graph alignments with gfainject). It then compares all combinations of two haplotypes from the graph to the sample alignments to find the best matching pair of haplotypes.

Usage

cosigt path_matrix.tsv sample.gafpack.gz bad_samples.txt prefix

• path_matrix.tsv - TSV file with path names and node coverages from odgi paths
• sample.gafpack.gz - GAF (graph alignment format) file for a sample compressed with pigz
• bad_samples.txt - Text file with names of paths to exclude (one per line)
• prefix - Prefix for output files

This will generate:

• prefix/combos.tsv - Cosine similarity scores for all haplotype combinations
• prefix/best_genotype.tsv - Best matching haplotype pair and score

Installation

Cosigt requires Go 1.16+ to install.

git clone https://github.com/user/cosigt
cd cosigt
go build

Algorithm

For each pair of haplotypes from the graph locus:

1. Sum the coverages for the pair
2. Calculate the cosine similarity between the summed coverages and the sample alignments
3. Sort pairs by cosine similarity to find best matching genotype

License

cosigt is released under the MIT License.