Usage
get.variants( file = "http://cgd.jax.org/tools/SNPtools/Build38/sanger.snps.NCBI38.txt.gz", chr, start, end, type = c("snp", "indel", "sv"), strains, polymorphic = TRUE, quality)
Arguments
file
Character, full path to the SNP file to use. Default is the file at the Center for Genome Dynamics at The Jackson Laboratory.
chr
Numeric vector, chr for each start and end position. Chr, start and end must all have the same length.
start
Numeric vector, start position in Mb or bp for each chr. Chr, start and end must all have the same length.
end
Numeric vector, end position in Mb or bp for each chr. Must be greater than or equal to the corresponding start value. Chr, start and end must all have the same length.
type
Character, with one of "snp", "indel", "sv". Indicates the type of variantes being queried.
strains
Character vector, listing the strains to retrieve. The names can be obtained from get.strains(). Default returns all strains.
polymorphic
Boolean. Default = TRUE. If TRUE, retrieve only SNPs that are polymorphic among the requested strains. If FALSE, return all SNPs in the requested interval(s).
quality
Integer, denoting the confidence levels to return. This looks at the quality column of all requested strains and takes values greater than or equal to the given number. Look at the documentation for the SNP file you are using for details on the quality score. Default returns all SNPs.