Combining probabilistic alignments with read pair information improves accuracy of split-alignments.
Bioinformatics
; 34(21): 3631-3637, 2018 11 01.
Article
em En
| MEDLINE
| ID: mdl-29790902
ABSTRACT
Motivation Split-alignments provide base-pair-resolution evidence of genomic rearrangements. In practice, they are found by first computing high-scoring local alignments, parts of which are then combined into a split-alignment. This approach is challenging when aligning a short read to a large and repetitive reference, as it tends to produce many spurious local alignments leading to ambiguities in identifying the correct split-alignment. This problem is further exacerbated by the fact that rearrangements tend to occur in repeat-rich regions. Results:
We propose a split-alignment technique that combats the issue of ambiguous alignments by combining information from probabilistic alignment with positional information from paired-end reads. We demonstrate that our method finds accurate split-alignments, and that this translates into improved performance of variant-calling tools that rely on split-alignments. Availability and implementation An open-source implementation is freely available at https//bitbucket.org/splitpairedend/last-split-pe. Supplementary information Supplementary data are available at Bioinformatics online.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Software
/
Genômica
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2018
Tipo de documento:
Article