Dataset Information
PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.
Ontology highlight
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.
SUBMITTER: Nato AQ
PROVIDER: S-EPMC4668752 | biostudies-literature | 2015 Dec
REPOSITORIES: biostudies-literature
Publications
PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.
Bioinformatics (Oxford, England) 20150730 23
<h4>Motivation</h4>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 lin ...[more]
