Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree.

ABSTRACT:

Background

Two types of approaches are mainly considered for the repeat number estimation in short tandem repeat (STR) regions from high-throughput sequencing data: approaches directly counting repeat patterns included in sequence reads spanning the region and approaches based on detecting the difference between the insert size inferred from aligned paired-end reads and the actual insert size. Although the accuracy of repeat numbers estimated with the former approaches is high, the size of target STR regions is limited to the length of sequence reads. On the other hand, the latter approaches can handle STR regions longer than the length of sequence reads. However, repeat numbers estimated with the latter approaches is less accurate than those with the former approaches.

Results<

SUBMITTER: Kojima K 

PROVIDER: S-EPMC5009668 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature