What is a track?
A track is the place to display your data files in JBrowse Linear View. For this tutorial we're going to add a gene track, an alignments track, and a variants track. We're just going to use basic configuration, but check the links for the track types to see what kinds of things you can configure in them.
For genes, we'll use a GFF3 file of the NCBI RefSeq human genes. The link is https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz
For alignments, we're going to use on the 1000 Genomes sample NA12878. We'll use a CRAM file (BAM is also supported), and the link is https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram
For variants, we'll use a VCF of the 1000 Genomes variant calls (note that this VCF contains all samples, not just NA12878). The link is https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz
Creating track configurations with the CLI
Open "config.json" again and look at the tracks that were generated. You can see that again, it has guessed index locations for you, which you can change if needed. Create a new file called "tracks.js" and copy the tracks array into it and have it exported, like this:
Now update "index.html" to import this file.