title: PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.
abstract: BACKGROUND
  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.
  
  
  METHODS
  PBAP scripts may be downloaded from http://faculty.washington.edu/wijsman/software.shtml.
  
  
  BACKGROUND
  wijsman@uw.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Division of Medical Genetics, Department of Medicine.
authors.forename: Alejandro Q
authors.initials: AQ
authors.lastname: Nato
authors.affiliation: Division of Medical Genetics, Department of Medicine.
authors.forename: Nicola H
authors.initials: NH
authors.lastname: Chapman
authors.affiliation: Division of Medical Genetics, Department of Medicine.
authors.forename: Harkirat K
authors.initials: HK
authors.lastname: Sohi
authors.affiliation: Division of Medical Genetics, Department of Medicine.
authors.forename: Hiep D
authors.initials: HD
authors.lastname: Nguyen
authors.affiliation: Department of Psychiatry and Behavioral Sciences.
authors.forename: Zoran
authors.initials: Z
authors.lastname: Brkanac
authors.affiliation: Division of Medical Genetics, Department of Medicine, Department of Biostatistics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Ellen M
authors.initials: EM
authors.lastname: Wijsman
mesh_terms: D000067877:Autism Spectrum Disorder / Q000235:genetics*; D005260:Female; D008040:Genetic Linkage; D005819:Genetic Markers; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011786:Quality Control; D012984:Software
chemical_list: D005819:Genetic Markers