Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches.

ABSTRACT:

Background

Calling germline SNP variants from bisulfite-converted sequencing data poses a challenge for conventional software, which have no inherent capability to dissociate true polymorphisms from artificial mutations induced by the chemical treatment. Nevertheless, SNP data is desirable both for genotyping and to understand the DNA methylome in the context of the genetic background. The confounding effect of bisulfite conversion however can be conceptually resolved by observing differences in allele counts on a per-strand basis, whereby artificial mutations are reflected by non-complementary base pairs.

Results

Herein, we present a computational pre-processing approach for adapting sequence alignment data, thus indirectly enabling downstream analysis on a per-strand basis

SUBMITTER: Nunn A 

PROVIDER: S-EPMC9237988 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature