Entering edit mode
3.5 years ago
ansakim20
▴
10
Hi I am new to this forum and bioinformatics, I am trying to understand the functionality of the VariantAnnotation package in Bioconductor R, in the filterVcf vignette the files are read in from the package as follows
###################################################
### code chunk number 5: createFilteredFile
###################################################
file.gz <- system.file("extdata", "chr7-sub.vcf.gz",
package="VariantAnnotation")
file.gz.tbi <- system.file("extdata", "chr7-sub.vcf.gz.tbi",
package="VariantAnnotation")
can someone please explain, how do I read in my own vcf and tbi file?
Following is the link to the R code