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.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)

[Package PureCN version 2.0.2 Index]