BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing.

ABSTRACT:

Motivation

While many pipelines have been developed for calling genotypes using RNA-sequencing (RNA-Seq) data, they all have adapted DNA genotype callers that do not model biases specific to RNA-Seq such as allele-specific expression (ASE).

Results

Here, we present Bayesian beta-binomial mixture model (BBmix), a Bayesian beta-binomial mixture model that first learns the expected distribution of read counts for each genotype, and then deploys those learned parameters to call genotypes probabilistically. We benchmarked our model on a wide variety of datasets and showed that our method generally performed better than competitors, mainly due to an increase of up to 1.4% in the accuracy of heterozygous calls, which may have a big impact in reducing false positive rate in applicat

SUBMITTER: Vigorito E 

PROVIDER: S-EPMC10318392 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature