Alejandro Q Nato1, Nicola H Chapman1, Harkirat K Sohi1, Hiep D Nguyen1, Zoran Brkanac2, Ellen M Wijsman3. 1. Division of Medical Genetics, Department of Medicine. 2. Department of Psychiatry and Behavioral Sciences. 3. Division of Medical Genetics, Department of Medicine, Department of Biostatistics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Abstract
MOTIVATION: Huge genetic datasets with dense marker panels are now common. With the availability of sequence data and recognition of importance of rare variants, smaller studies based on pedigrees are again also common. Pedigree-based samples often start with a dense marker panel, a subset of which may be used for linkage analysis to reduce computational burden and to limit linkage disequilibrium between single-nucleotide polymorphisms (SNPs). Programs attempting to select markers for linkage panels exist but lack flexibility. RESULTS: We developed a pedigree-based analysis pipeline (PBAP) suite of programs geared towards SNPs and sequence data. PBAP performs quality control, marker selection and file preparation. PBAP sets up files for MORGAN, which can handle analyses for small and large pedigrees, typically human, and results can be used with other programs and for downstream analyses. We evaluate and illustrate its features with two real datasets. AVAILABILITY AND IMPLEMENTATION: PBAP scripts may be downloaded from http://faculty.washington.edu/wijsman/software.shtml. CONTACT: wijsman@uw.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Huge genetic datasets with dense marker panels are now common. With the availability of sequence data and recognition of importance of rare variants, smaller studies based on pedigrees are again also common. Pedigree-based samples often start with a dense marker panel, a subset of which may be used for linkage analysis to reduce computational burden and to limit linkage disequilibrium between single-nucleotide polymorphisms (SNPs). Programs attempting to select markers for linkage panels exist but lack flexibility. RESULTS: We developed a pedigree-based analysis pipeline (PBAP) suite of programs geared towards SNPs and sequence data. PBAP performs quality control, marker selection and file preparation. PBAP sets up files for MORGAN, which can handle analyses for small and large pedigrees, typically human, and results can be used with other programs and for downstream analyses. We evaluate and illustrate its features with two real datasets. AVAILABILITY AND IMPLEMENTATION: PBAP scripts may be downloaded from http://faculty.washington.edu/wijsman/software.shtml. CONTACT: wijsman@uw.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: E E Marchani; N H Chapman; C Y K Cheung; K Ankenman; I B Stanaway; H H Coon; D Nickerson; R Bernier; Z Brkanac; E M Wijsman Journal: Hum Hered Date: 2013-04-11 Impact factor: 0.444
Authors: Tara C Matise; Jose Luis Ambite; Steven Buyske; Christopher S Carlson; Shelley A Cole; Dana C Crawford; Christopher A Haiman; Gerardo Heiss; Charles Kooperberg; Loic Le Marchand; Teri A Manolio; Kari E North; Ulrike Peters; Marylyn D Ritchie; Lucia A Hindorff; Jonathan L Haines Journal: Am J Epidemiol Date: 2011-08-11 Impact factor: 4.897
Authors: Weiva Sieh; Saonli Basu; Audrey Q Fu; Joseph H Rothstein; Paul A Scheet; William C L Stewart; Yun J Sung; Elizabeth A Thompson; Ellen M Wijsman Journal: BMC Genet Date: 2005-12-30 Impact factor: 2.797
Authors: Adam C Naj; Honghuang Lin; Badri N Vardarajan; Simon White; Daniel Lancour; Yiyi Ma; Michael Schmidt; Fangui Sun; Mariusz Butkiewicz; William S Bush; Brian W Kunkle; John Malamon; Najaf Amin; Seung Hoan Choi; Kara L Hamilton-Nelson; Sven J van der Lee; Namrata Gupta; Daniel C Koboldt; Mohamad Saad; Bowen Wang; Alejandro Q Nato; Harkirat K Sohi; Amanda Kuzma; Li-San Wang; L Adrienne Cupples; Cornelia van Duijn; Sudha Seshadri; Gerard D Schellenberg; Eric Boerwinkle; Joshua C Bis; Josée Dupuis; William J Salerno; Ellen M Wijsman; Eden R Martin; Anita L DeStefano Journal: Genomics Date: 2018-05-29 Impact factor: 5.736
Authors: Rafael A Nafikov; Alejandro Q Nato; Harkirat Sohi; Bowen Wang; Lisa Brown; Andrea R Horimoto; Badri N Vardarajan; Sandra M Barral; Giuseppe Tosto; Richard P Mayeux; Timothy A Thornton; Elizabeth Blue; Ellen M Wijsman Journal: Genet Epidemiol Date: 2018-06-03 Impact factor: 2.135
Authors: D T Truong; L D Shriberg; S D Smith; K L Chapman; A R Scheer-Cohen; M M C DeMille; A K Adams; A Q Nato; E M Wijsman; J D Eicher; J R Gruen Journal: Hum Genet Date: 2016-08-17 Impact factor: 4.132
Authors: Beate Peter; Ellen M Wijsman; Alejandro Q Nato; Mark M Matsushita; Kathy L Chapman; Ian B Stanaway; John Wolff; Kaori Oda; Virginia B Gabo; Wendy H Raskind Journal: PLoS One Date: 2016-04-27 Impact factor: 3.240