findHighQualitySNPs: Find High Quality SNPs

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

Find High Quality SNPs

Description

Function to extract high quality SNPs from the mapping bias database. Useful for generating fingerprinting panels etc.

Usage

findHighQualitySNPs(
  mapping.bias.file,
  max.bias = 0.2,
  min.pon = 2,
  triallelic = FALSE,
  vcf.file = NULL,
  genome
)

Arguments

mapping.bias.file	Generated by calculateMappingBiasVcf.
max.bias	Maximum mapping bias
min.pon	Minimum number of normal samples, useful to get reliable mapping bias.
triallelic	By default, ignore positions with multiple alt alleles.
vcf.file	Optional VCF file (for example dbSNP). Needs to be bgzip and tabix processed.
genome	See readVcf

Value

A GRanges object with mapping bias passing filters. If vcf.file is provided, it will be the variants in the corresponding file overlapping with the passed variants.

Author(s)

Markus Riester

Examples

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

lima1/PureCN documentation built on Nov. 22, 2024, 6:07 a.m.