lineage 4.5.0

tools for analyzing and exploring genetic relationships

lineage

tools for analyzing and exploring genetic relationships 🧬

lineage strives to be an easy-to-use and accessible open-source library for genetic genealogy

Features

Shared DNA Analysis

• Find shared DNA between individuals using genetic maps from the HapMap Project and 1000 Genomes Project
• Compute centiMorgans (cMs) of shared DNA with configurable thresholds
• Detect IBD1 (half-identical) and IBD2 (fully identical) regions
• Visualize shared DNA segments across all chromosomes
• Find discordant SNPs inconsistent with Mendelian inheritance patterns

Shared Gene Analysis

• Identify genes shared between individuals with the same genetic variations
• Determine which genes produce the same proteins across related individuals

Synthetic Data Generation

• Generate realistic synthetic genotype data for related individuals
• Create parent-child pairs with proper single-allele inheritance
• Create sibling pairs with realistic meiotic recombination patterns

Supported Genotype Files

lineage supports all genotype files supported by snps.

Installation

lineage is available on the Python Package Index. Install lineage (and its required Python dependencies) via pip:

$ pip install lineage

Examples

The examples below demonstrate the core features of lineage. For detailed explanations of genetic concepts like IBD (Identity By Descent), centiMorgans, and how to interpret results, see the Concepts Guide.

Optional: To see file save notifications, configure logging before running examples:

import logging
logging.basicConfig(level=logging.INFO, format='%(message)s')

To try these examples, first generate some sample data:

>>> from lineage import Lineage
>>> l = Lineage()
>>> paths = l.create_example_datasets()

Load Individuals

Load genotype files and create Individual objects:

>>> parent = l.create_individual('Parent', paths['parent'])
>>> child = l.create_individual('Child', paths['child'])

Each Individual inherits from snps.SNPs, providing access to all SNPs properties and methods:

>>> parent.build
37
>>> parent.assembly
'GRCh37'
>>> parent.count
899992

Find Discordant SNPs

Identify SNPs inconsistent with Mendelian inheritance between parent and child:

>>> discordant_snps = l.find_discordant_snps(parent, child, save_output=True)  # doctest: +SKIP

The example datasets include a small number of simulated genotyping errors (~0.01%) to demonstrate discordant SNP detection.

Find Shared DNA

Parent-Child Example

Compute shared DNA segments and generate a visualization:

>>> results = l.find_shared_dna([parent, child])  # doctest: +SKIP

For parent-child relationships, all shared DNA appears on one chromosome only (IBD1), representing the chromosome inherited from that parent (~3400-3700 cM total):

Sibling Example

Analyze siblings using a population-specific genetic map:

>>> sibling1 = l.create_individual('Sibling1', paths['sibling1'])  # doctest: +SKIP
>>> sibling2 = l.create_individual('Sibling2', paths['sibling2'])  # doctest: +SKIP
>>> results = l.find_shared_dna([sibling1, sibling2], shared_genes=True, genetic_map="CEU")  # doctest: +SKIP

Siblings share DNA on one chromosome (IBD1) and both chromosomes (IBD2), reflecting segments where they inherited the same DNA from one or both parents:

Documentation

Documentation is available here.

Acknowledgements

Thanks to Whit Athey, Ryan Dale, Binh Bui, Jeff Gill, Gopal Vashishtha, CS50. This project was historically validated using data from openSNP.

lineage incorporates code and concepts generated with the assistance of various generative AI tools (including but not limited to ChatGPT, Grok, and Claude). ✨

License

lineage is licensed under the MIT License.