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vanquish

The goal of vanquish is to detect whether a sample with variant information is contaminated by another sample from the same species.

Example

This is a basic example which shows you how to detect whether vcf_example is contaminated:

## basic example code
library('vanquish')
data(vcf_example)
result <- defcon(file = vcf_example)
print(result$stat)
#>               Name       LOH       HomVar     HetVar  HomRate   HighRate
#> 1 sssc_test.vcf.gz 0.7248322 0.0001565125 0.02757586 0.536965 0.05350195
#>     HetRate    LowRate    AvgLL
#> 1 0.3608949 0.04669261 -2.01978
print(result$result)
#>               Name Class Regression
#> 1 sssc_test.vcf.gz     1  0.7131992

Given class = 1, vcf_example is considered to be contaminated.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.