iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data.
Brief Bioinform
; 22(3)2021 05 20.
Article
en En
| MEDLINE
| ID: mdl-32436933
ABSTRACT
Whole exome sequencing (WES) is a powerful approach for discovering sequence variants in cancer cells but its time effectiveness is limited by the complexity and issues of WES data analysis. Here we present iWhale, a customizable pipeline based on Docker and SCons, reliably detecting somatic variants by three complementary callers (MuTect2, Strelka2 and VarScan2). The results are combined to obtain a single variant call format file for each sample and variants are annotated by integrating a wide range of information extracted from several reference databases, ultimately allowing variant and gene prioritization according to different criteria. iWhale allows users to conduct a complex series of WES analyses with a powerful yet customizable and easy-to-use tool, running on most operating systems (macOs, GNU/Linux and Windows). iWhale code is freely available at https//github.com/alexcoppe/iWhale and the docker image is downloadable from https//hub.docker.com/r/alexcoppe/iwhale.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Biología Computacional
/
Mutación
/
Neoplasias
Límite:
Humans
Idioma:
En
Revista:
Brief Bioinform
Asunto de la revista:
BIOLOGIA
/
INFORMATICA MEDICA
Año:
2021
Tipo del documento:
Article