ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
Bioinformatics
; 29(14): 1809-10, 2013 Jul 15.
Article
em En
| MEDLINE
| ID: mdl-23681124
ABSTRACT
SUMMARY:
Direct comparisons of assembled short-read stacks are one way to identify single-nucleotide variants. Single-nucleotide variant detection is especially challenging across samples with different read depths (e.g. RNA-Seq) and high-background levels (e.g. selection experiments). We present ACCUSA2 to identify variant positions where nucleotide frequency spectra differ between two samples. To this end, ACCUSA2 integrates quality scores for base calling and read mapping into a common framework. Our benchmarks demonstrate that ACCUSA2 is superior to a state-of-the-art SNV caller in situations of diverging read depths and reliably detects subtle differences among sample nucleotide frequency spectra. Additionally, we show that ACCUSA2 is fast and robust against base quality score deviations.AVAILABILITY:
ACCUSA2 is available free of charge to academic users and may be obtained from https//bbc.mdc-berlin.de/software. CONTACT christoph.dieterich@mdc-berlin.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Variação Genética
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Software
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Sequenciamento de Nucleotídeos em Larga Escala
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2013
Tipo de documento:
Article