calculateMappingBiasGatk4: Calculate Mapping Bias from GATK4 GenomicsDB

View source: R/calculateMappingBiasVcf.R

calculateMappingBiasGatk4R 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.normals.assign.betafit = 3,
  min.normals.position.specific.fit = 10,
  min.median.coverage.betafit = 5,
  num.betafit.clusters = 9,
  min.betafit.rho = 1e-04,
  max.betafit.rho = 0.2,
  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.normals.assign.betafit

Minimum number of normals with heterozygous SNPs to assign to a beta binomal fit cluster

min.normals.position.specific.fit

Minimum normals to use position-specific beta-binomial fits. Otherwise only clustered fits are used.

min.median.coverage.betafit

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

num.betafit.clusters

Maximum number of beta binomial fit clusters

min.betafit.rho

Minimum dispersion factor rho

max.betafit.rho

Maximum dispersion factor rho

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)


lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.