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ROADTRIPS specifications

Information


Unique identifier OMICS_24091
Name ROADTRIPS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A genotype data file, a phenotype information file, a kinship coefficient file and a prevalence file.
Output data A file including a summary of the phenotype file information, the prevalence values used in the calculation, and a list of characteristics for each marker, a file containing a list with the top 20 SNPs with the smallest p-values for each of the 3 tests, a file giving the statistics results for each SNP, a file with the complete p-values for each SMP and an error file.
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 2.0
Stability Beta
Maintained Yes

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Documentation


Maintainers


  • person_outline Timothy Thornton
  • person_outline Sara McPeek

Publication for ROADTRIPS

ROADTRIPS citations

 (12)
call_split

Identifying genome wide immune gene variation underlying infectious disease in wildlife populations – a next generation sequencing approach in the gopher tortoise

2018
BMC Genomics
PMCID: 5775545
PMID: 29351737
DOI: 10.1186/s12864-018-4452-0
call_split See protocol

[…] indels as synonymous or non-synonymous using snpEff v4.0e []. We performed case/control association tests with PLINK v1.07 [], analyzing SNPs and indels separately. We repeated association test using ROADTRIPS v2.0 [], which controls for unknown population structure and individual relatedness. […]

library_books

Bacterial Genetic Architecture of Ecological Interactions in Co culture by GWAS Taking Escherichia coli and Staphylococcus aureus as an Example

2017
Front Microbiol
PMCID: 5712204
PMID: 29230205
DOI: 10.3389/fmicb.2017.02332

[…] In this study, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. By analyzing […]

library_books

A Pragmatic Test for Detecting Association between a Dichotomous Trait and the Genotypes of Affected Families, Controls and Independent Cases

2017
Front Genet
PMCID: 5422425
PMID: 28536599
DOI: 10.3389/fgene.2017.00049

[…] in the number of cases and controls is likely to increase the rate of cryptic relatedness and the extent of unreported population substructure. Although, modern methods like GMMAT (Chen et al., ) and ROADTRIPS (Thornton and McPeek, ) can account for some (if not all) of these potential confounders while incorporating covariates and unphenotyped samples, these methods typically do not model the tra […]

library_books

Characterizing the genetic basis of bacterial phenotypes using genome wide association studies: a new direction for bacteriology

2014
Genome Med
PMCID: 4295408
PMID: 25593593
DOI: 10.1186/s13073-014-0109-z

[…] test was used to correct for genetic background in discovering SNPs that are associated with beta-lactam resistance in two genetically different S. pneumoniae population clusters. Alam et al. [] used ROADTRIPS [], a regression-based approach that incorporates corrections for both known and inferred population structure.Two phylogeny-based approaches for association have been developed specifically […]

library_books

Comparison of Methods to Account for Relatedness in Genome Wide Association Studies with Family Based Data

2014
PLoS Genet
PMCID: 4102448
PMID: 25033443
DOI: 10.1371/journal.pgen.1004445

[…] Thornton and McPeek implemented a ‘RObust Association- Detection Test for Related Individuals with Population Substructure’ in a package called ROADTRIPS. ROADTRIPS can be thought of as an extension of their previously-proposed Maximum Quasi-Likelihood Statistic (MQLS) . Both MQLS and ROADTRIPS construct adjusted versions of standard case/con […]

library_books

Dissecting Vancomycin Intermediate Resistance in Staphylococcus aureus Using Genome Wide Association

2014
Genome Biol Evol
PMCID: 4040999
PMID: 24787619
DOI: 10.1093/gbe/evu092

[…] c substitutions (i.e., structured by population) that were noninformative in association studies. To identify SNPs within this set that were associated with vancomycin-intermediate resistance we used ROADTRIPS (), a regression-based approach that also accounts for unknown and known population structure in analyses of binary (ROADTRIPS) or continuous (QROADTRIPS) outcomes. We found that no SNP was […]

Citations

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ROADTRIPS institution(s)
Department of Biostatistics, University of Washington, Seattle, WA, USA; Department of Statistics, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA
ROADTRIPS funding source(s)
Supported, in part, by the University of California President’s Postdoctoral Fellowship and the Lamond Family Foundation Postdoctoral Fellowship and by National Institutes of Health grant R01 HG001645.

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