Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing.

ABSTRACT:

Background

Inherent sources of error and bias that affect the quality of sequence data include index hopping and bias towards the reference allele. The impact of these artefacts is likely greater for low-coverage data than for high-coverage data because low-coverage data has scant information and many standard tools for processing sequence data were designed for high-coverage data. With the proliferation of cost-effective low-coverage sequencing, there is a need to understand the impact of these errors and bias on resulting genotype calls from low-coverage sequencing.

Results

We used a dataset of 26 pigs sequenced both at 2× with multiplexing and at 30× without multiplexing to show that index hopping and bias towards the reference allele due to alignment had little impact on

SUBMITTER: Ros-Freixedes R 

PROVIDER: S-EPMC6293637 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature