AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.

ABSTRACT:

Background

Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA.

Results

We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ances

SUBMITTER: Schaefer NK 

PROVIDER: S-EPMC5381037 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature