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Bioinformatics. 2015 Dec 1;31(23):3790-8. doi: 10.1093/bioinformatics/btv444. Epub 2015 Jul 30.

PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.

Author information

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.

PMID:
26231429
PMCID:
PMC4668752
DOI:
10.1093/bioinformatics/btv444
[Indexed for MEDLINE]
Free PMC Article

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