Empirical Bayes Single Nucleotide Variant Calling

Identifies single nucleotide variants in next-generation sequencing data by estimating their local false discovery rates. For more details, see Karimnezhad, A. and Perkins, T. J. (2024) .

SNVLFDR

Empirical Bayes Single Nucleotide Variant Calling for Next Generation Sequencing Data

LFDR-based Variant Calling

Identifies single nucleotide variants in next-generation sequencing data by estimating their local false discovery rates. For more details, see https://doi.org/10.1038/s41598-024-51958-z.

Installation

The package can be installed from the GitHub repository

devtools::install_github("empiricalbayes/SNVLFDR")

Getting Started

You can load SNVLFDR as follows:

library(SNVLFDR)

How to run SNVLFDR to call variants on an example data.

bam_input <- system.file("extdata", "bam_input.csv", package="SNVLFDR")
bedfile <- system.file("extdata", "regions.bed", package="SNVLFDR")
BQ.T=20
MQ.T=20
pi0.initial=0.95
AF.T=0.01
DP.T=10
LFDR.T=0.01
error=NULL
method='empirical'
epsilon=0.01
output=get_LFDRs(bam_input,bedfile,BQ.T,MQ.T,pi0.initial,AF.T,DP.T,LFDR.T,error,method,epsilon)

#Estimated LFDRs
output$estimated.LFDRs

#Estimated proportion on non-mutant sites
output$estimated.pi0

#Filtered Bam matrix that includes estimated LFDRs
output$filtered.bam


## How to run SNVLFDR to prioritize variants called by another variant caller
bam_path <- system.file("extdata", "bam_input.csv", package="SNVLFDR")
calls_path <- system.file("extdata", "calls.vcf", package="SNVLFDR")
output=get_LFDRs_given_caller(bam_input=bam_path,calls=calls_path,LFDR.T=0.01,error=NULL)

#Updated VCF file that includes estimated LFDRs
output$updated.vcf

References

Karimnezhad, A and Perkins, T.J. (2024) Empirical Bayes single nucleotide variant-calling for next-generation sequencing data. Scientific Reports 14, 1550, https://doi.org/10.1038/s41598-024-51958-z