Literature DB >> 32345333

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery.

Johannes Köster1,2,3, Louis J Dijkstra4,5, Tobias Marschall6, Alexander Schönhuth7,8.   

Abstract

Entities:  

Keywords:  Bayesian latent variable model; FDR control; Somatic; Tumor/normal; Variant calling

Mesh：

Year:  2020        PMID： 32345333      PMCID： PMC7187499          DOI： 10.1186/s13059-020-01993-6

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


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  38 in total

Review 1.  A survey of sequence alignment algorithms for next-generation sequencing.

Authors:  Heng Li; Nils Homer
Journal:  Brief Bioinform       Date:  2010-05-11       Impact factor: 11.622

2.  Uncertainty in homology inferences: assessing and improving genomic sequence alignment.

Authors:  Gerton Lunter; Andrea Rocco; Naila Mimouni; Andreas Heger; Alexandre Caldeira; Jotun Hein
Journal:  Genome Res       Date:  2007-12-11       Impact factor: 9.043

3.  A framework for variation discovery and genotyping using next-generation DNA sequencing data.

Authors:  Mark A DePristo; Eric Banks; Ryan Poplin; Kiran V Garimella; Jared R Maguire; Christopher Hartl; Anthony A Philippakis; Guillermo del Angel; Manuel A Rivas; Matt Hanna; Aaron McKenna; Tim J Fennell; Andrew M Kernytsky; Andrey Y Sivachenko; Kristian Cibulskis; Stacey B Gabriel; David Altshuler; Mark J Daly
Journal:  Nat Genet       Date:  2011-04-10       Impact factor: 38.330

4.  Identification of neutral tumor evolution across cancer types.

Authors:  Marc J Williams; Benjamin Werner; Chris P Barnes; Trevor A Graham; Andrea Sottoriva
Journal:  Nat Genet       Date:  2016-01-18       Impact factor: 38.330

5.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

Review 6.  The causes and consequences of genetic heterogeneity in cancer evolution.

Authors:  Rebecca A Burrell; Nicholas McGranahan; Jiri Bartek; Charles Swanton
Journal:  Nature       Date:  2013-09-19       Impact factor: 49.962

7.  DELLY: structural variant discovery by integrated paired-end and split-read analysis.

Authors:  Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M Stütz; Vladimir Benes; Jan O Korbel
Journal:  Bioinformatics       Date:  2012-09-15       Impact factor: 6.937

8.  Discovering motifs that induce sequencing errors.

Authors:  Manuel Allhoff; Alexander Schönhuth; Marcel Martin; Ivan G Costa; Sven Rahmann; Tobias Marschall
Journal:  BMC Bioinformatics       Date:  2013-04-10       Impact factor: 3.169

9.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.

Authors:  Kristian Cibulskis; Michael S Lawrence; Scott L Carter; Andrey Sivachenko; David Jaffe; Carrie Sougnez; Stacey Gabriel; Matthew Meyerson; Eric S Lander; Gad Getz
Journal:  Nat Biotechnol       Date:  2013-02-10       Impact factor: 54.908

10.  Genome-wide somatic variant calling using localized colored de Bruijn graphs.

Authors:  Giuseppe Narzisi; André Corvelo; Kanika Arora; Ewa A Bergmann; Minita Shah; Rajeeva Musunuri; Anne-Katrin Emde; Nicolas Robine; Vladimir Vacic; Michael C Zody
Journal:  Commun Biol       Date:  2018-03-22
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  3 in total

1.  Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing.

Authors:  Alicia Isabell Tüns; Till Hartmann; Simon Magin; Rocío Chamorro González; Anton George Henssen; Sven Rahmann; Alexander Schramm; Johannes Köster
Journal:  Front Genet       Date:  2022-05-30       Impact factor: 4.772

2.  Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo.

Authors:  David Lähnemann; Johannes Köster; Ute Fischer; Arndt Borkhardt; Alice C McHardy; Alexander Schönhuth
Journal:  Nat Commun       Date:  2021-11-18       Impact factor: 14.919

3.  Analysis of low-level somatic mosaicism reveals stage and tissue-specific mutational features in human development.

Authors:  Ja Hye Kim; Shinwon Hwang; Hyeonju Son; Dongsun Kim; Il Bin Kim; Myeong-Heui Kim; Nam Suk Sim; Dong Seok Kim; Yoo-Jin Ha; Junehawk Lee; Hoon-Chul Kang; Jeong Ho Lee; Sangwoo Kim
Journal:  PLoS Genet       Date:  2022-09-19       Impact factor: 6.020
  3 in total

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