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2 hours ago by

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

<h6>#</h6>

code chunk number 5: createFilteredFile

<h6>#</h6>

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

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



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