Home

Welcome to the gramtools wiki!

Overview

Gramtools builds a directed acyclical graph (DAG) of genetic variation from a population of genomes. Given sequence data from a haploid or diploid individual, alleles on the graph are annotated with coverage information. A personalized reference for the sample being studied can then be inferred from the annotated graph. The infered reference is the closest recombinant of genomes in the graph.

Future Enhancements

Future work will extend functionality to support the following:

• mixed ploidy inference
• novel variant discovery.

Toy Dataset Example

1. Get data

• Download data: gramtools_toy_dataset.zip
• Extract
• $ cd gramtools_toy_dataset

2. Build

$ gramtools build --gram_dir ./gram --vcf ./vcf_file.vcf --ref ./NC_000962.2_modified.fasta

3. Genotype

$ gramtools genotype -i ./gram -o ./run --reads ./random_simulated_reads