Three-stage quality control strategies for DNA re-sequencing data

作者: Y. Guo , F. Ye , Q. Sheng , T. Clark , D. C. Samuels

DOI: 10.1093/BIB/BBT069

关键词:

摘要: … , heterozygosity rate and novel SNP number evaluate overall the SNP quality at a per … quality and mapping quality filters can also be used to prevent bad reads from contributing to SNP …

参考文章(46)
Qi Liu, Yan Guo, Jiang Li, Jirong Long, Bing Zhang, Yu Shyr, Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data BMC Genomics. ,vol. 13, pp. 1- 8 ,(2012) , 10.1186/1471-2164-13-S8-S8
Caroline Michot, Carine Le Goff, Alice Goldenberg, Avinash Abhyankar, Céline Klein, Esther Kinning, Anne-Marie Guerrot, Philippe Flahaut, Alice Duncombe, Genevieve Baujat, Stanislas Lyonnet, Caroline Thalassinos, Patrick Nitschke, Jean-Laurent Casanova, Martine Le Merrer, Arnold Munnich, Valérie Cormier-Daire, None, Exome Sequencing Identifies PDE4D Mutations as Another Cause of Acrodysostosis American Journal of Human Genetics. ,vol. 90, pp. 740- 745 ,(2012) , 10.1016/J.AJHG.2012.03.003
Qian Zhou, Xiaoquan Su, Anhui Wang, Jian Xu, Kang Ning, QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data PLoS ONE. ,vol. 8, pp. e60234- ,(2013) , 10.1371/JOURNAL.PONE.0060234
K. Wang, M. Li, H. Hakonarson, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Research. ,vol. 38, ,(2010) , 10.1093/NAR/GKQ603
Timothy Daley, Andrew D Smith, Predicting the molecular complexity of sequencing libraries Nature Methods. ,vol. 10, pp. 325- 327 ,(2013) , 10.1038/NMETH.2375
Yongchao Liu, Jan Schröder, Bertil Schmidt, Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics. ,vol. 29, pp. 308- 315 ,(2013) , 10.1093/BIOINFORMATICS/BTS690
Yan Guo, Jirong Long, Jing He, Chung-I Li, Qiuyin Cai, Xiao-Ou Shu, Wei Zheng, Chun Li, Exome sequencing generates high quality data in non-target regions BMC Genomics. ,vol. 13, pp. 194- 194 ,(2012) , 10.1186/1471-2164-13-194
Sergey I Nikolaev, Donata Rimoldi, Christian Iseli, Armand Valsesia, Daniel Robyr, Corinne Gehrig, Keith Harshman, Michel Guipponi, Olesya Bukach, Vincent Zoete, Olivier Michielin, Katja Muehlethaler, Daniel Speiser, Jacques S Beckmann, Ioannis Xenarios, Thanos D Halazonetis, C Victor Jongeneel, Brian J Stevenson, Stylianos E Antonarakis, Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma Nature Genetics. ,vol. 44, pp. 133- 139 ,(2012) , 10.1038/NG.1026
Cecilia Lanave, Stefania Tommasi, Giuliano Preparata, Cecilia Saccone, Transition and transversion rate in the evolution of animal mitochondrial DNA BioSystems. ,vol. 19, pp. 273- 283 ,(1986) , 10.1016/0303-2647(86)90004-3