This is an R package that compares a user's single nucleotide variant list to calls derived from ultra-deep whole-genome and validation data generated from the AML31 tumor, relapse, and matched normal.
#install dependencies
install.packages(c("venneuler","devtools"))
library(devtools)
install_github("genome/aml31Benchmarking")
library(aml31Benchmarking)
#Run an example with included mock data
data(testData)
benchmark(testData,"/tmp/outTable","/tmp/out.pdf")
#Run on your data
read.table("myData","/path/to/table/output","/path/to/plot/output.pdf")
Descriptions of how the 'gold' and 'platinum' lists were generated can be found in this publication: (insert publication info here).
Sequence data for those who wish to make their own variant calls is available through dbGaP (insert accession numbers here)
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