Allelic-Imbalance

Last updated: 3 years ago (view history), Time to read: 2 mins

Description

These code block examples can be used to generate an allelic-imblance figure as seen in VisCom.

Use: Displays the allelic imbalance of the heterozygous SNP markers in a tumor genome as compared to this patient’s germline genome, as a way of indicating loss-of-heterozygosity. ProteinPaint Google Docs

URL Key Example

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.

Be sure to update lines 1, 3, 8, 9, and 10

{
    "genome": "hg19",
    "nativetracks": "RefGene",
    "position": "chr17:7565096-7590856",
    "block": true,
    "tracks": [
        {
            "type": "aicheck",
            "name": "Track name",
            "url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/zYf5XqZ04fBKk6VbQFQbv8P8BG8xyGyQp3FzFkG8z/\aicheck.gz",
            "indexURL": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/b0YJQx5F110Z90P9q7ZZFXqv03Gv41Qfy0yX7gYK/\aicheck.gz.tbi"
        }
    ]
}

File Key Example

warning

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.

Be sure to update lines 1, 3, 8, and 9

{
    "genome": "hg19",
    "nativetracks": "RefGene",
    "position": "chr17:7565096-7590856",
    "block": true,
    "tracks": [
        {
            "type": "aicheck",
            "name": "Track name",
            "file": "proteinpaint_demo\/hg19\/aicheck\/file.gz" 
        }
    ]
}