variantspark (version 0.1.1)

vs_read_vcf: Reading a VCF file

Description

The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project. The vs_read_vcf() reads this format and returns a jobj object from VCFFeatureSource scala class.

Usage

vs_read_vcf(vsc, path)

Arguments

vsc

A variantspark connection.

path

The file's path.

Value

spark_jobj, shell_jobj

Examples

# NOT RUN {
 
# }
# NOT RUN {
library(sparklyr)

sc <- spark_connect(master = "local")
vsc <- vs_context(sc)

hipster_vcf <- vs_read_vcf(vsc, 
                           system.file("extdata/hipster.vcf.bz2",
                                       package = "variantspark"))

hipster_vcf 
# }
# NOT RUN {
# }