Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments.

ABSTRACT: The human reference assembly remains incomplete due to the underrepresentation of repeat-rich sequences that are found within centromeric regions and acrocentric short arms. Although these sequences are marginally represented in the assembly, they are often fully represented in whole-genome short-read datasets and contribute to inappropriate alignments and high read-depth signals that localize to a small number of assembled homologous regions. As a consequence, these regions often provide artifactual peak calls that confound hypothesis testing and large-scale genomic studies. To address this problem, we have constructed mapping targets that represent roughly 8% of the human genome generally omitted from the human reference assembly. By integrating these data into standard mapping and peak-

SUBMITTER: Miga KH 

PROVIDER: S-EPMC4787761 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature