Protocols

PBAP specifications

Information


Unique identifier OMICS_10129
Name PBAP
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Wijsman E.M.

Publication for PBAP

PBAP citations

 (2)
library_books

Multipoint genome wide linkage scan for nonword repetition in a multigenerational family further supports chromosome 13q as a locus for verbal trait disorders

2016
Hum Genet
PMCID: 5065602
PMID: 27535846
DOI: 10.1007/s00439-016-1717-z

[…] he 1000 Genomes Project Consortium ) to determine linkage disequilibrium (LD) and minor allele frequencies (MAF) between markers for marker sub-selection.We used the pedigree based analysis pipeline (PBAP) to sub-select genetic markers for pedigree quality control (QC) and for interfacing with MORGAN (Thompson ) to calculate inheritance vectors (IV) used for linkage analysis (Nato et al. ). Use of […]

call_split

Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech

2016
PLoS One
PMCID: 4847873
PMID: 27120335
DOI: 10.1371/journal.pone.0153864
call_split See protocol

[…] with genotyping errors were removed from the analysis. Files were formatted for MCMC linkage analysis and an ideal set of SNPs was chosen for a marker panel with the Pedigree-Based Analysis Pipeline (PBAP) [], targeting marker spacing of 0.5 centimorgan (cM), minor allele frequency (MAF) > 0.2, and LD between markers < 0.04. Minor allele frequencies (MAFs) for the SNP arrays were based on the 1000 […]

PBAP institution(s)
Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
PBAP funding source(s)
This work was supported by the National Institutes of Health (R01 MH092367, R01 MH094293, R01 AG039700, R37 GM046255, P50 AG005136 and U01 AG016976).

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