Vcfgl: a flexible genotype likelihood simulator for VCF/BCF files.

ABSTRACT:

Motivation

Accurate quantification of genotype uncertainty is pivotal in ensuring the reliability of genetic inferences drawn from NGS data. Genotype uncertainty is typically modeled using Genotype Likelihoods (GLs), which can help propagate measures of statistical uncertainty in base calls to downstream analyses. However, the effects of errors and biases in the estimation of GLs, introduced by biases in the original base call quality scores or the discretization of quality scores, as well as the choice of the GL model, remain under-explored.

Results

We present vcfgl, a versatile tool for simulating genotype likelihoods associated with simulated read data. It offers a framework for researchers to simulate and investigate the uncertainties and biases associated with the quant

SUBMITTER: Altinkaya I 

PROVIDER: S-EPMC11968323 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature