loadVCFs: loadVCFs

In jpuntomarcos/CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

loadVCFs

Description

Loads VCFs files

Usage

loadVCFs(
  vcf.files,
  sample.names = NULL,
  cnvs.gr,
  min.total.depth = 10,
  regions.to.exclude = NULL,
  vcf.source = NULL,
  ref.support.field = NULL,
  alt.support.field = NULL,
  list.support.field = NULL,
  homozygous.range = c(90, 100),
  heterozygous.range = c(28, 72),
  exclude.indels = TRUE,
  genome = "hg19",
  exclude.non.canonical.chrs = TRUE,
  verbose = TRUE
)

Arguments

vcf.files	vector of VCFs paths. Both .vcf and .vcf.gz extensions are allowed.
sample.names	Sample names vector containing sample names for each vcf.files. If NULL, sample name will be obtained from the VCF sample column. (Defaults to NULL)
cnvs.gr	GRanges object containg CNV calls. Call loadCNVcalls to obtain it. Only those variants in regions affected by CNVs will be loaded to speed up the load.
min.total.depth	Minimum total depth. Variants under this value will be excluded. (Defaults to 10)
regions.to.exclude	A GRanges object defining the regions for which the variants should be excluded. Useful for defining known difficult regions like pseudogenes where the allele frequency is not trustable. (Defaults to NULL)
vcf.source	VCF source, i.e., the variant caller used to generate the VCF file. If set, the loadSNPsFromVCF function will not try to recognize the source. (Defaults to NULL)
ref.support.field	Reference allele depth field. (Defaults to NULL)
alt.support.field	Alternative allele depth field. (Defaults to NULL)
list.support.field	Allele support field in a list format: reference allele, alternative allele. (Defaults to NULL)
homozygous.range	Homozygous range. Variants not in the homozygous/heterozygous intervals will be excluded. (Defaults to c(90, 100))
heterozygous.range	Heterozygous range. Variants not in the homozygous/heterozygous intervals will be excluded. (Defaults to c(28, 72))
exclude.indels	Whether to exclude indels when loading the variants. TRUE is the recommended value given that indels frequency varies in a different way than SNVs. (Defaults to TRUE)
genome	The name of the genome. (Defaults to "hg19")
exclude.non.canonical.chrs	Whether to exclude non canonical chromosomes (Defaults to TRUE)
verbose	Whether to show information messages. (Defaults to TRUE)

Details

Loads VCF files and computes alt allele frequency for each variant. It uses loadSNPsFromVCF function load the data and identify the correct VCF format for allele frequency computation.

If sample.names is not provided, the sample names included in the VCF itself will be used. Both single-sample and multi-sample VCFs are accepted, but when multi-sample VCFs are used, sample.names parameter must be NULL.

If vcf is not compressed with bgzip, the function compresses it and generates the .gz file. If .tbi file does not exist for a given VCF file, the function also generates it. All files are generated in a temporary folder.

Value

A list where names are the sample names, and values are the GRanges objects for each sample.

Note

Important: Compressed VCF must be compressed with [bgzip ("block gzip") from Samtools htslib](http://www.htslib.org/doc/bgzip.html) and not using the standard Gzip utility.

Examples

# Load CNVs data (required by loadVCFs to speed up the load process)
cnvs.file <- system.file("extdata", "DECoN.CNVcalls.csv", package = "CNVfilteR", mustWork = TRUE)
cnvs.gr <- loadCNVcalls(cnvs.file = cnvs.file, chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample")

# Load VCFs data
vcf.files <- c(system.file("extdata", "variants.sample1.vcf.gz", package = "CNVfilteR", mustWork = TRUE),
               system.file("extdata", "variants.sample2.vcf.gz", package = "CNVfilteR", mustWork = TRUE))
vcfs <- loadVCFs(vcf.files, cnvs.gr = cnvs.gr)

jpuntomarcos/CNVfilteR documentation built on Oct. 6, 2023, 12:37 a.m.