Creates the necessary configuration string for an indexed VCF file so that it can be used in a JBrowse custom linear genome view.
track_variant(track_data, assembly)the URL to the VCF file
the config string generated by assembly
a character vector of stringified VariantTrack JSON configuration
It is important to note that while only the VCF file is
passed as an argument, tracks_variant assumes that a VCF
index of the same name is located with the file
For example:
track_alignments("data/variants.vcf")
Assumes that data/variants.vcf.tbi also exists.
This is a JBrowse 2 convention, and the default naming output of tabix
For more information on creating an index with tabix, visit https://www.htslib.org/
assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
track_variant("variants.vcf", assembly)
#> [1] "{ \"type\": \"VariantTrack\", \"name\": \"variants\", \"assemblyNames\": [\"hg19\"], \"trackId\": \"hg19_variants\", \"adapter\": { \"type\": \"VcfTabixAdapter\", \"vcfGzLocation\": { \"uri\": \"variants.vcf\" }, \"index\": { \"location\": { \"uri\": \"variants.vcf.tbi\" } }}}"