Readme.md

In genome/aml31Benchmarking: Benchmark variant calls against curated variant lists from aml31

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.

Installation

#install dependencies
install.packages(c("venneuler","devtools"))
library(devtools)
install_github("genome/aml31Benchmarking")

Usage

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)

genome/aml31Benchmarking documentation built on May 17, 2019, 1:11 a.m.