Usage
read.vcf(vcf.file, gr, chr = 1, start = 4, end = 4.5, strains, return.val = c("allele", "number"), return.qual = TRUE, csq = FALSE)
Arguments
vcf.file
Character string containing full path to a Sanger SNP, Indel or structural variant VCF file.
gr
GRanges object containing one or more ranges to query. Use either this argument or the chr, start and end arguments, but not both.
chr
Character or numeric vector containing mouse chromosome IDs to query.
start
Numeric vector containing the start position on each chromosome to query. Must be the same length as chr. If the value is less than 200, it is assumed to be in Mb. Values greater than 200 are assumed to be in bp.
end
Numeric vector containing the end position on each chromosome to query. Must be the same length as chr. If the value is less than 200, it is assumed to be in Mb. Values greater than 200 are assumed to be in bp.
strains
Character vector containing strain names, as listed in the vcf.file, to retrieve. If missing, then all strains are returned. Use get.vcf.strains
to get the strain names from the VCF file.
return.val
Character string that is either "allele", which returns the nucleotide allele calls, or "number", which returns numeric values.
return.qual
Boolean that is TRUE if the quality columns should be returned.
csq
Boolean that is TRUE if the consequence column should be returned.