igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
MIT License
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How to turn off downsampling option #86

Closed canna1998 closed 11 months ago

canna1998 commented 1 year ago

By default, the Downsampling option is enabled in the generated html file. I have checked the previous issues, it seems that there was no downsample function before, can I turn this option off and display all reads now?

jrobinso commented 1 year ago

You can do this, and many more things, by using the --track-config option to specify your tracks rather than just listing them by file path. See the example using --track-config option in the README. The track options are describe in the igv.js wiki. Specifically, for your case you would set samplingDepth in an alignment track config to a very large number, for example

Example of trackConfig.json

[
  {
    "name": "Variants",
    "url": "test/data/variants/variants.vcf.gz"
  },
  {
    "name": "Alignments",
    "url": "test/data/variants/recalibrated.bam",
    "samplingDepth": 1000000,
    "color": "rgb(0,150,150)"
  },
  {
    "name": "Genes",
    "type": "",
    "url": "test/data/hg38/refGene.txt.gz",
    "indexURL": "test/data/hg38/refGene.txt.gz.tbi"
  }
]