read_vcf | R Documentation |
Wrapper around Bioconductor VariantAnnotation. Reads VCF into GRanges or data.table format
read_vcf( fn, gr = NULL, hg = "hg19", geno = NULL, swap.header = NULL, verbose = FALSE, add.path = FALSE, tmp.dir = "~/temp/.tmpvcf", ... )
fn |
argument to parse via bcftools |
gr |
GRanges input GRanges (default = NULL) |
hg |
string Human reference genome (default = 'hg19') |
geno |
boolean Flag whether to pull the genotype information information in the GENO vcf fields (default = NULL) |
swap.header |
string Pathn to another VCF file (in case of VCF with malformed header)(default = NULL) |
verbose |
boolean Flag (default = FALSE) |
add.path |
boolean Flag to add the path of the current VCF file to the output (default = FALSE) |
tmp.dir |
string Path to directory for temporary files (default = '~/temp/.tmpvcf') |
... |
extra parameters |
Marcin Imielinski
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