read_vcf | R Documentation |
VCF (Variant Call Format) file format is used to store variation data and its metadata. Based on the used analysis program (e.g. GATK, freebayes, etc...), details within the VCF file can slightly differ. For example, type of mutation is not mentioned as output for certain variant analysis programs. the "read_vcf" function, ignores the first header/metadata lines and directly converts the data into a tidy dataframe. The function will extract the type of mutation. By absence, it will derive the type of mutation from the "ref" and "alt" column.
read_vcf(
file,
parse_info = FALSE,
col_names = def_names("vcf"),
col_types = def_types("vcf")
)
file |
Either a path to a file, a connection, or literal data (either a single string or a raw vector). Files ending in Literal data is most useful for examples and tests. To be recognised as
literal data, the input must be either wrapped with Using a value of |
parse_info |
if set to 'TRUE', the read_vcf function will split all the metadata stored in the "info" column and stores it into separate columns. By default it is set to 'FALSE'. |
col_names |
column names to use. Defaults to |
col_types |
column types to use. Defaults to |
dataframe
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