get_LFDRs_given_caller {SNVLFDR}

Estimates LFDR values per mutant site detected by a desired variant caller

Description

Based on a given read count matrix and a list of calls made by a desired variant caller, estimates LFDRs that corresponds to each genomic site. It further classifies sites to either mutant or non-mutant sites by comparing their estimated LFDRs with an LFDR cut-off value. The cut-off value as well as error rates can be defined by users.

Usage

get_LFDRs_given_caller(bam_input, calls, LFDR.T, error)

Arguments

bam_input

Path to an original BAM file used to call variants. The file must be in the format of a csv file generated by bam-readcount (https://github.com/genome/bam-readcount). See Examples.

calls

Path to a vcf file generated by a variant caller. The first and second columns of this file have to be CHR names and positions, respectively.

LFDR.T

A number between 0 and 1. It can be set to 0 to include all sites. Otherwise, this threshold excludes sites with an LFDR below the specified threshold. If no value is specified, it will be set to 0.01 by default.

error

Error rate between 0 and 1. If it is set to NULL, a weighted average of average base call quality and average mapping quality per site will be calculated. Otherwise, it may be set to 0.01 or a desired error vector can be introduced by the user.

Value

A list. Slot estimated.LFDRs returns estimated LFDRs for all sites in the input file. Slot updated.bam adds estimated LFDRs, model errors and a mutant variable (indicating whether each site is detected to be a mutant (1) or non-mutant (0) site) to the input bam file.

References

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

Examples

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)