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how to read in vcf.gz and tbi file for filtervcf using VariantAnnotation in R

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

https://bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/inst/doc/VariantAnnotation.R

r snp
• 2,301 views • link
updated by GenoMax GenoMax • written by ansakim20 • ansakim20

1 answer

I figured it out since the file was in my machine, I just had to assign the path of that file

myfile <- path to my file
• 0 views • link
updated by GenoMax GenoMax • written by ansakim20 • ansakim20

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