iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data.
Bioinformatics
Cancer
Docker
Pipeline
Whole exome sequencing
Journal
Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837
Informations de publication
Date de publication:
20 05 2021
20 05 2021
Historique:
received:
27
12
2019
revised:
27
03
2020
accepted:
30
03
2020
pubmed:
22
5
2020
medline:
16
11
2021
entrez:
22
5
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32436933
pii: 5840042
doi: 10.1093/bib/bbaa065
pmc: PMC8557746
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Références
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Sci Rep. 2015 Sep 18;5:14283
pubmed: 26381817
Cell. 2018 Aug 9;174(4):1034-1035
pubmed: 30096302
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
Genome Med. 2018 Mar 28;10(1):25
pubmed: 29592813
Int J Cancer. 2008 Oct 1;123(7):1483-90
pubmed: 18636562
Science. 2004 Oct 8;306(5694):269-71
pubmed: 15472075
Haematologica. 2019 Sep;104(9):e406-e409
pubmed: 30819919
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18261-6
pubmed: 17114293
J Clin Pathol. 2002 Aug;55(8):596-601
pubmed: 12147653
BMC Res Notes. 2015 Mar 08;8:72
pubmed: 25889517
Front Genet. 2018 Feb 26;9:35
pubmed: 29535759
Blood. 2007 Nov 15;110(10):3753-62
pubmed: 17698635
Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544
pubmed: 29790989
BMC Genomics. 2016 Sep 02;17:703
pubmed: 27590916
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Front Oncol. 2019 Apr 16;9:263
pubmed: 31058077
Science. 2013 Mar 29;339(6127):1546-58
pubmed: 23539594
Immunity. 2000 Jul;13(1):73-84
pubmed: 10933396
Genome Res. 2015 Jun;25(6):918-25
pubmed: 25883319
Nat Rev Cancer. 2019 Nov;19(11):639-650
pubmed: 31455892
Hum Mutat. 2018 Apr;39(4):579-587
pubmed: 29316027
Blood. 2016 Aug 25;128(8):1093-100
pubmed: 27325104
Genome Med. 2017 Apr 18;9(1):35
pubmed: 28420412
Cancer Res. 2008 Nov 1;68(21):8705-14
pubmed: 18974112
Front Genet. 2012 Mar 15;3:35
pubmed: 22435069
BMC Bioinformatics. 2016 Nov 8;17(Suppl 12):341
pubmed: 28185561
Nat Genet. 2011 May;43(5):491-8
pubmed: 21478889
Hum Genomics. 2014 Jun 30;8:11
pubmed: 24980617
Hum Genomics. 2014 Jul 30;8:14
pubmed: 25078893
PLoS Comput Biol. 2019 Apr 29;15(4):e1006981
pubmed: 31034466
Leukemia. 2017 May;31(5):1243-1246
pubmed: 28167832
F1000Res. 2018 Aug 24;7:1338
pubmed: 30254741
Nat Methods. 2015 Jul;12(7):623-30
pubmed: 25984700
Br J Haematol. 2018 Jul;182(1):135-138
pubmed: 28485469
Bioinformatics. 2019 Sep 1;35(17):3157-3159
pubmed: 30649191
Nucleic Acids Res. 2020 Jan 8;48(D1):D941-D947
pubmed: 31584097
BMC Med Genomics. 2019 May 16;12(1):63
pubmed: 31096972
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Bioinformatics. 2013 Sep 1;29(17):2208-10
pubmed: 23803469
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Int J Cancer. 2018 Nov 15;143(10):2525-2536
pubmed: 29992558
Trends Cancer. 2018 Sep;4(9):634-642
pubmed: 30149881
PLoS One. 2015 Nov 10;10(11):e0142631
pubmed: 26555578