304 related articles for article (PubMed ID: 28185561)
1. Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.
do Valle ÍF; Giampieri E; Simonetti G; Padella A; Manfrini M; Ferrari A; Papayannidis C; Zironi I; Garonzi M; Bernardi S; Delledonne M; Martinelli G; Remondini D; Castellani G
BMC Bioinformatics; 2016 Nov; 17(Suppl 12):341. PubMed ID: 28185561
[TBL] [Abstract][Full Text] [Related]
2. Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers.
Hofmann AL; Behr J; Singer J; Kuipers J; Beisel C; Schraml P; Moch H; Beerenwinkel N
BMC Bioinformatics; 2017 Jan; 18(1):8. PubMed ID: 28049408
[TBL] [Abstract][Full Text] [Related]
3. Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.
Xu H; DiCarlo J; Satya RV; Peng Q; Wang Y
BMC Genomics; 2014 Mar; 15():244. PubMed ID: 24678773
[TBL] [Abstract][Full Text] [Related]
4. A three-caller pipeline for variant analysis of cancer whole-exome sequencing data.
Liu ZK; Shang YK; Chen ZN; Bian H
Mol Med Rep; 2017 May; 15(5):2489-2494. PubMed ID: 28447726
[TBL] [Abstract][Full Text] [Related]
5. Detection of Somatic Mutations in Exome Sequencing of Tumor-only Samples.
Hsu YC; Hsiao YT; Kao TY; Chang JG; Shieh GS
Sci Rep; 2017 Nov; 7(1):15959. PubMed ID: 29162841
[TBL] [Abstract][Full Text] [Related]
6. Variant callers for next-generation sequencing data: a comparison study.
Liu X; Han S; Wang Z; Gelernter J; Yang BZ
PLoS One; 2013; 8(9):e75619. PubMed ID: 24086590
[TBL] [Abstract][Full Text] [Related]
7. Halvade somatic: Somatic variant calling with Apache Spark.
Decap D; de Schaetzen van Brienen L; Larmuseau M; Costanza P; Herzeel C; Wuyts R; Marchal K; Fostier J
Gigascience; 2022 Jan; 11(1):. PubMed ID: 35022699
[TBL] [Abstract][Full Text] [Related]
8. An evaluation of copy number variation detection tools for cancer using whole exome sequencing data.
Zare F; Dow M; Monteleone N; Hosny A; Nabavi S
BMC Bioinformatics; 2017 May; 18(1):286. PubMed ID: 28569140
[TBL] [Abstract][Full Text] [Related]
9. A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference.
Cornish A; Guda C
Biomed Res Int; 2015; 2015():456479. PubMed ID: 26539496
[TBL] [Abstract][Full Text] [Related]
10. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Koboldt DC; Zhang Q; Larson DE; Shen D; McLellan MD; Lin L; Miller CA; Mardis ER; Ding L; Wilson RK
Genome Res; 2012 Mar; 22(3):568-76. PubMed ID: 22300766
[TBL] [Abstract][Full Text] [Related]
11. Practicability of detecting somatic point mutation from RNA high throughput sequencing data.
Sheng Q; Zhao S; Li CI; Shyr Y; Guo Y
Genomics; 2016 May; 107(5):163-9. PubMed ID: 27046520
[TBL] [Abstract][Full Text] [Related]
12. Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools.
Alganmi N; Abusamra H
PLoS One; 2023; 18(8):e0288371. PubMed ID: 37535628
[TBL] [Abstract][Full Text] [Related]
13. Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.
Krøigård AB; Thomassen M; Lænkholm AV; Kruse TA; Larsen MJ
PLoS One; 2016; 11(3):e0151664. PubMed ID: 27002637
[TBL] [Abstract][Full Text] [Related]
14. Challenges in exome analysis by LifeScope and its alternative computational pipelines.
Pranckevičiene E; Rančelis T; Pranculis A; Kučinskas V
BMC Res Notes; 2015 Sep; 8():421. PubMed ID: 26346699
[TBL] [Abstract][Full Text] [Related]
15. Construction of a combinatorial pipeline using two somatic variant calling methods for whole exome sequence data of gastric cancer.
Kohmoto T; Masuda K; Naruto T; Tange S; Shoda K; Hamada J; Saito M; Ichikawa D; Tajima A; Otsuji E; Imoto I
J Med Invest; 2017; 64(3.4):233-240. PubMed ID: 28954988
[TBL] [Abstract][Full Text] [Related]
16. Evaluating somatic tumor mutation detection without matched normal samples.
Teer JK; Zhang Y; Chen L; Welsh EA; Cress WD; Eschrich SA; Berglund AE
Hum Genomics; 2017 Sep; 11(1):22. PubMed ID: 28870239
[TBL] [Abstract][Full Text] [Related]
17. BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity.
Cantarel BL; Weaver D; McNeill N; Zhang J; Mackey AJ; Reese J
BMC Bioinformatics; 2014 Apr; 15():104. PubMed ID: 24725768
[TBL] [Abstract][Full Text] [Related]
18. Impact of post-alignment processing in variant discovery from whole exome data.
Tian S; Yan H; Kalmbach M; Slager SL
BMC Bioinformatics; 2016 Oct; 17(1):403. PubMed ID: 27716037
[TBL] [Abstract][Full Text] [Related]
19. Bioinformatics Analysis of Whole Exome Sequencing Data.
Ulintz PJ; Wu W; Gates CM
Methods Mol Biol; 2019; 1881():277-318. PubMed ID: 30350213
[TBL] [Abstract][Full Text] [Related]
20. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.
Favero F; Joshi T; Marquard AM; Birkbak NJ; Krzystanek M; Li Q; Szallasi Z; Eklund AC
Ann Oncol; 2015 Jan; 26(1):64-70. PubMed ID: 25319062
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]