VCF
These code block examples can be used to generate a figure using vcf data as seen in VisCom.
These code block examples can be used to generate a figure using vcf data as seen in VisCom.
Use: This track localizes the variant data on reference genomes and can render frequency data for cohorts. ProteinPaint Google Docs
Warning
If you are using DNAnexus links, be sure to extend the duration. See our manage data section. In order to render .gz files they must also have the .tbi file associated. What happens is that the ProteinPaint looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.
If you are using DNAnexus links, be sure to extend the duration. See our manage data section. In order to render .gz files they must also have the .tbi file associated. What happens is that the ProteinPaint looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.
URL Parameter EXAMPLE
Be sure to update lines 1, 3, 8, 9 and 10
{
"genome": "hg38",
"nativetracks": "RefGene",
"position": "BCL11A",
"block": true,
"tracks": [
{
"type": "vcf",
"name": "Track name",
"url": "https:\/\/westus.dl.azure.dnanex.us\/F\/DSYM\/QBPkx3pb635bV1z7z9XK3PpkzVp8XY67yKjj2v6Z\/SJACT004_D.WholeGenome.g.vcf.gz",
"indexURL": "https:\/\/westus.dl.azure.dnanex.us\/F\/DSYM\/3zkPkpvb54Q5PzJ1k039BP52Zv4kz99p2GpBQ89Y\/SJACT004_D.WholeGenome.g.vcf.gz.tbi"
}
]
}
Warning
If you are using a path on the HPC, the file must exist in a directory in the
If you are using a path on the HPC, the file must exist in a directory in the
/tp directory.
For more details, see our manage data section.Path to file EXAMPLE
Be sure to update lines 1, 3, 8, and 9
{
"genome": "hg38",
"nativetracks": "RefGene",
"position": "BCL11A",
"block": true,
"tracks": [
{
"type": "vcf",
"name": "Track name",
"file": "proteinpaint_demo\/hg38\/GP\/TCGA_DLBC.vcf.gz"
}
]
}
t-SNE (Sample Scatterplot)
These code block examples can be used to generate a t-SNE as seen in VisCom.
ProteinPaint
ProteinPaint is a web application for simultaneously visualizing genetic lesions (including sequence mutations and gene fusions) and RNA expression in pediatric cancers. You can find the ProteinPaint paper here.