Edge effects in calling variants from targeted amplicon sequencing.

ABSTRACT:

Background

Analysis of targeted amplicon sequencing data presents some unique challenges in comparison to the analysis of random fragment sequencing data. Whereas reads from randomly fragmented DNA have arbitrary start positions, the reads from amplicon sequencing have fixed start positions that coincide with the amplicon boundaries. As a result, any variants near the amplicon boundaries can cause misalignments of multiple reads that can ultimately lead to false-positive or false-negative variant calls.

Results

We show that amplicon boundaries are variant calling blind spots where the variant calls are highly inaccurate. We propose that an effective strategy to avoid these blind spots is to incorporate the primer bases in obtaining read alignments and post-processing of the

SUBMITTER: Satya RV 

PROVIDER: S-EPMC4302139 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature