calculateMappingBiasVcf: Calculate Mapping Bias

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

Description

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

Usage

calculateMappingBiasVcf(
  normal.panel.vcf.file,
  min.normals = 1,
  min.normals.betafit = 7,
  min.median.coverage.betafit = 5,
  yieldSize = 5000,
  genome
)

Arguments

normal.panel.vcf.file	Combined VCF file of a panel of normals, reference and alt counts as AD genotype field. Should be compressed and indexed with bgzip and tabix, respectively.
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
yieldSize	See TabixFile
genome	See readVcf

Value

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

Author(s)

Markus Riester

Examples

normal.panel.vcf <- system.file("extdata", "normalpanel.vcf.gz", package="PureCN")
bias <- calculateMappingBiasVcf(normal.panel.vcf, genome = "h19")
saveRDS(bias, "mapping_bias.rds")

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.