Exploring mechanisms to traverse compressed Variant Calling Formatted files remotely: without downloading them, and without a tbi file with content indexes. The rationale is the same advanced for digital pathology in imagebox2 by relying on range requests. For parsing full files see old project at IBL.

Although the real action is in the console, this page will be used to test the JavaScript vcf SDK. To do so, select the URL of the remote VCF file (or use default test VCF file borrowed from Tollefson 2019), and then try different methods. For examples of the real-world challenge see clinVar, snp or 1000genomes.

Passing parameters via URL

You may pass parameters to read and filter some VCF file URL of your choice. The following parameters are available:

  • URL (Mandatory) - VCF file url
  • Range - The interval that you want to read (Default value is 0,1000 )
  • Query - The chromosome and position you want to search in the VCF file (Example: 7,151040280)
  • Example of how to assemble the parameters: https://episphere.github.io/vcf/#url=https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz&range=0,10000&query=7,151040280
  • You will find three examples of parameters in the demonstration links at the top of this page

Data

The data below will be used to demonstrate the main functions of our library, it contains all SNPs found in the Human genome. Make sure that the CORS is enabled in the data server, otherwise is not possible accessing it.

1 - Reading a slice of the data

Choose an interval to read, then an object of VCF library will be initialized and will return the corresponding data with the chosen byte range.

up to

2 - Finding chromosomes and positions

Choose a specific chromosome and position to search across the vcf file. Our search algorithm uses an strategy to optimize the search, returning the respective results in miliseconds.
Examples to try it out: chromosome 7 and position 151040280 (7,151040280), chromosome 10 and position 133421085 (10,133421085), chromosome 17 and position 7675353 (17,7675353).

Chromosome:
Position: