loadSNPsFromVCF {CNVfilteR} | R Documentation |
Loads SNPs (SNVs/indels) from a VCF file
loadSNPsFromVCF( vcf.file, vcf.source = NULL, ref.support.field = NULL, alt.support.field = NULL, list.support.field = NULL, regions.to.filter = NULL, genome = "hg19", exclude.non.canonical.chrs = TRUE, verbose = TRUE )
vcf.file |
VCF file path |
vcf.source |
VCF source, i.e., the variant caller used to generate the VCF file. If set, the 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) |
regions.to.filter |
The regions to which limit the VCF import. It can be used to speed up the import process. (Defaults to NULL) |
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) |
Given a VCF file path, the function recognizes the variant caller source to decide which fields should be used to calculate
ref/alt support and allelic frequency (see return
). Current supported variant callers are VarScan2, Strelka/Strelka2, freebayes,
HaplotypeCaller, UnifiedGenotyper and Torrent Variant Caller.
Optionally, the fields where the data is stored can be manually set by using the parameters ref.support.field
,
alt.support.field
and list.support.field
Requirement: a TabixFile (.tbi) should exists in the same directory of the VCF file.
A list where names are sample names, and values are GRanges
objects containing the variants for each sample, including the following metadata columns:
ref.support
: Reference allele depth field
alt.support
: Alternative allele depth field
alt.freq
: allelic frequency
total.depth
: total depth
vcf.file <- system.file("extdata", "variants.sample1.vcf.gz", package = "CNVfilteR", mustWork = TRUE) vcf <- loadSNPsFromVCF(vcf.file)