Modeling biases from low-pass genome sequencing to enable accurate population genetic inferences.
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ABSTRACT:
SUBMITTER: Fonseca EM
PROVIDER: S-EPMC11291017 | biostudies-literature | 2024 Jul
REPOSITORIES: biostudies-literature
Publications
Modeling biases from low-pass genome sequencing to enable accurate population genetic inferences.
Fonseca Emanuel M EM Tran Linh N LN Mendoza Hannah H Gutenkunst Ryan N RN
bioRxiv : the preprint server for biology 20240723
Low-pass genome sequencing is cost-effective and enables analysis of large cohorts. However, it introduces biases by reducing heterozygous genotypes and low-frequency alleles, impacting subsequent analyses such as demographic history inference. We developed a probabilistic model of low-pass biases from the Genome Analysis Toolkit (GATK) multi-sample calling pipeline, and we implemented it in the population genomic inference software dadi. We evaluated the model using simulated low-pass datasets ...[more]
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