calculateMappingBiasGatk4 {PureCN}R Documentation

Calculate Mapping Bias from GATK4 GenomicsDB

Description

Function calculate mapping bias for each variant in the provided panel of normals GenomicsDB.

Usage

calculateMappingBiasGatk4(
  workspace,
  reference.genome,
  min.normals = 1,
  min.normals.betafit = 7,
  min.median.coverage.betafit = 5,
  AF.info.field = "AF"
)

Arguments

workspace

Path to the GenomicsDB created by GenomicsDBImport

reference.genome

Reference FASTA file.

min.normals

Minimum number of normals with heterozygous SNP for calculating position-specific mapping bias.

min.normals.betafit

Minimum number of normals with heterozygous SNP fitting a beta distribution

min.median.coverage.betafit

Minimum median coverage of normals with heterozygous SNP for fitting a beta distribution

AF.info.field

Field in the workspace that stores the allelic fraction

Value

A GRanges object with mapping bias and number of normal samples with this variant.

Author(s)

Markus Riester

Examples


## Not run:  
resources_file <- system.file("extdata", "gatk4_pon_db.tgz", 
    package = "PureCN")
tmp_dir <- tempdir()
untar(resources_file, exdir = tmp_dir)
workspace <- file.path(tmp_dir, "gatk4_pon_db")
bias <- calculateMappingBiasGatk4(workspace, "hg19")
saveRDS(bias, "mapping_bias.rds")
unlink(tmp_dir, recursive=TRUE)

## End(Not run)
[Package PureCN version 1.22.2 Index]