Finding cryptic relationships to boost disease gene detection

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TRIBES

This is documentation to TRIBES version 0.2+. For the the documentation for older version 0.1 please check https://github.com/aehrc/TRIBES/tree/branch-0.1 .

TRIBES is a user-friendly platform for relatedness detection in genomic data. TRIBES is the first tool which is both accurate (up to 7th degree) and combines essential data processing steps in a single platform.

We demonstrate the accuracy of TRIBES in our publications here and here

Briefly, input data to TRIBES is quality control filtered, joint sample VCF. TRIBES then follows these steps:

  1. The VCF is filtered using quality metrics contained within the VCF file.

  2. The resultant VCF is then phased using BEAGLE.

  3. IBD Segments are then estimated using GERMLINE.

  4. Artefactual IBD is masked using a reference file by adjusting segment endpoints.

  5. Adjusted IBD Segments are then summed to estimate relationships.

  6. TRIBES returns result files, including .csv of estimated relationships.

To facilitate ease-of-use we employ ‘Snakemake’, a workflow tool which enables flexibility and reproducibility.

The full TRIBES pipeline is described in detail in Supplementary Material .

Learn more

Watch a short video introducing TRIBES and its applications TRIBES video

See documentation for more information on installing and using TRIBES

Code Snippets

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knitr::opts_chunk$set(echo = TRUE, warning=FALSE, fig.width=12, fig.height=8)
R Markdown From line 9 of notebooks/compare_vs_true_rel.Rmd 
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library(ggplot2)
library(dplyr)
library(tribes.tools)
R Markdown ggplot2 dplyr From line 13 of notebooks/compare_vs_true_rel.Rmd 
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#Snakemake interface
args = list()
if (exists('snakemake')) {
    args = list(estimatedRelFile = snakemake@input$estRel, 
                trueRelFile = snakemake@input$trueRel)

} else {
    warning("Not running with snakemake. Using test arguments!!!")
    args = list(estimatedRelFile = '~/tmp/tribes/TFEur/FF-EUR-15-30-2-mut_BiSnp_EurAF:0.01_LD_PH_GRM-allchr_IBD.csv', 
                trueRelFile = '~/tmp/tribes/TFEur/FF-EUR-15-30-2-mut_relations.txt')
}
print(args)
R Markdown Snakemake From line 19 of notebooks/compare_vs_true_rel.Rmd 
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estimatedRelations <- normalizeRelations(read.csv(args$estimatedRelFile, header = TRUE, stringsAsFactors = FALSE) %>% 
    mutate(EstDegree = as.relDegree(EstDegree)))
trueRelations <- readRelations(args$trueRelFile)
estimateRelationsWithTrue <- left_join(trueRelations, estimatedRelations, by=c('Id1', 'Id2')) %>%
    mutate(
        EstDegree = na.replace(EstDegree, as.relDegree('UR')), 
        IBD0.cM = na.replace(IBD0.cM, 1.0)
    )
head(estimateRelationsWithTrue)
R Markdown From line 34 of notebooks/compare_vs_true_rel.Rmd 
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#group and count by Known degree:Predicted degree combination
estimatedVsTruth <- estimateRelationsWithTrue %>%
  group_by(Degree, EstDegree) %>%
  count()

head(estimatedVsTruth)
R Markdown From line 46 of notebooks/compare_vs_true_rel.Rmd 
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#make plot comparing estimated to true degree - excluding unrelated as it distorts scale
print(
    ggplot(estimatedVsTruth, aes(Degree, EstDegree)) 
        + geom_point(aes(size = n)) 
        + geom_text(aes(label=n),hjust=0.5, vjust=-1, colour='red') 
        + theme_bw()
        + labs(title="Predicted vs True with UR",
                        y="Estimated degree of relationship",
                        x="Degree of reported relationship")
)
R Markdown ggplot2 From line 56 of notebooks/compare_vs_true_rel.Rmd 
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#make plot comparing estimated to true degree - excluding unrelated as it distorts scale
print(
    ggplot(estimatedVsTruth %>% filter(Degree != "UR") , aes(Degree, EstDegree)) 
        + geom_point(aes(size = n)) 
        + geom_text(aes(label=n),hjust=0.5, vjust=-1, colour='red') 
        + theme_bw()
        + labs(title="Predicted vs True no UR",
                        y="Estimated degree of relationship",
                        x="Degree of reported relationship")
)
R Markdown ggplot2 From line 70 of notebooks/compare_vs_true_rel.Rmd 
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shell:
    "echo 'Usage:' ;"
    "echo '    tribes -d <working dir> (estimate_degree|estimate_degree_vs_true)'"
SnakeMake From line 20 of branch-0.2/Snakefile 
1
__version__="0.2.0"
Python From line 1 of branch-0.2/_version.py
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/aehrc/TRIBES
Name: tribes
Version: v0.3.0dev1-1
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