read_vcfs_as_granges: Read VCF files into a GRangesList
In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description Usage Arguments Value Examples

This function reads Variant Call Format (VCF) files into a GRanges object and combines them in a GRangesList. In addition to loading the files, this function applies the same seqlevel style to the GRanges objects as the reference genome passed in the 'genome' parameter.

read_vcfs_as_granges(
  vcf_files,
  sample_names,
  genome,
  group = c("auto+sex", "auto", "sex", "circular", "all", "none"),
  type = c("snv", "indel", "dbs", "mbs", "all"),
  change_seqnames = TRUE
)

`vcf_files`	Character vector of VCF file names
`sample_names`	Character vector of sample names
`genome`	A string matching the name of a BSgenome library corresponding to the reference genome of your VCFs
`group`	Selector for a seqlevel group. All seqlevels outside of this group will be removed. Possible values: * 'all' for all chromosomes; * 'auto' for autosomal chromosomes; * 'sex' for sex chromosomes; * 'auto+sex' for autosomal + sex chromosomes (default); * 'circular' for circular chromosomes; * 'none' for no filtering, which results in keeping all seqlevels from the VCF file.
`type`	The mutation type that will be loaded. All other variants will be filtered out. Possible values: * 'snv' * 'indel' * 'dbs' * 'mbs' * 'all' This function assumes that dbs and mbs variants are present in the vcf as SNVs, which are positioned next to each other. If your dbs/mbs variants are called separately you should use type = 'all' to prevent incorrect filtering. In those cases SNVs could be selected per sample by something like: 'gr[width(gr) == 1]'
`change_seqnames`	Boolean. Whether to change the seqnamesStyle of the vcf to that of the BSgenome object. (default = TRUE)

A GRangesList containing the GRanges obtained from 'vcf_files'

## The example data set consists of three colon samples, three intestine
## samples and three liver samples.  So, to map each file to its appropriate
## sample name, we create a vector containing the sample names:
sample_names <- c(
  "colon1", "colon2", "colon3",
  "intestine1", "intestine2", "intestine3",
  "liver1", "liver2", "liver3"
)

## We assemble a list of files we want to load.  These files match the
## sample names defined above.
vcf_files <- list.files(system.file("extdata",
  package = "MutationalPatterns"
),
pattern = "sample.vcf", full.names = TRUE
)

## Get a reference genome BSgenome object.
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library("BSgenome")
library(ref_genome, character.only = TRUE)

## This function loads the files as GRanges objects.
## For backwards compatability reasons it only loads SNVs by default
vcfs <- read_vcfs_as_granges(vcf_files, sample_names, ref_genome)

## To load all variant types use:
vcfs <- read_vcfs_as_granges(vcf_files, sample_names, ref_genome, type = "all")

## Loading only indels can be done like this.

## Select data containing indels.
vcf_fnames <- list.files(system.file("extdata", package = "MutationalPatterns"),
  pattern = "blood.*vcf", full.names = TRUE
)
sample_names <- c("AC", "ACC55", "BCH")

## Read data and select only the indels.
## Other mutation types can be read in the same way.
read_vcfs_as_granges(vcf_fnames, sample_names, ref_genome, type = "indel")