The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
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.
The package can be installed from the GitHub repository
You can load SNVLFDR as follows:
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
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
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.
Health stats visible at Monitor.