Nato AQ, Chapman NH, Sohi HK, Nguyen HD, Brkanac Z, Wijsman EM. PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.
Bioinformatics 2015;
31:3790-8. [PMID:
26231429 PMCID:
PMC4668752 DOI:
10.1093/bioinformatics/btv444]
[Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/07/2015] [Accepted: 07/25/2015] [Indexed: 11/13/2022] Open
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.
Collapse