calculateMappingBiasGatk4: Calculate Mapping Bias from GATK4 GenomicsDB

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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.