This function reads the VCF file into R and converts it to a data.table format. While genomic range is given, HTSlib, a wrapped C library, reads directly from a region instead of loading the full VCF file to memory. It is mandatory to compress the VCF file using bgzip and create an index using tabix.
Usage
read_vcf(file, range = NULL)
Arguments
- file
The VCF file.
- range
To specify the range you want to read from the genome. e.g. "1:1000-100000" (genomic range), "1:12345"(single variant), "1:12345-12345" (single variant), NULL (all variants)
Value
A list which include a genotype matrix and a marker information data.table. Return NULL if no variant found withing given range.