PhredEM: a phred-score-informed genotype-calling approach for next-generation sequencing studies.

ABSTRACT: A fundamental challenge in analyzing next-generation sequencing (NGS) data is to determine an individual's genotype accurately, as the accuracy of the inferred genotype is essential to downstream analyses. Correctly estimating the base-calling error rate is critical to accurate genotype calls. Phred scores that accompany each call can be used to decide which calls are reliable. Some genotype callers, such as GATK and SAMtools, directly calculate the base-calling error rates from phred scores or recalibrated base quality scores. Others, such as SeqEM, estimate error rates from the read data without using any quality scores. It is also a common quality control procedure to filter out reads with low phred scores. However, choosing an appropriate phred score threshold is problematic as a too h

SUBMITTER: Liao P 

PROVIDER: S-EPMC5564424 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature