Updates:

  • vSampler now supports sampling on X chromosome.
  • vSampler now supports input file to be separated by commas.

vSampler is both a web-based tool and a local program to support matched control variant sampling. Given input variants, vSampler could randomly sample control variants with matched minor allele frequency (MAF), distance to closet transcription start site (DTCT), number of nearby genes, number of variants in LD, GC content and many other properties. These matched random controls could be used to construct null distribution for GWAS enrichment analysis to estimate significance of enrichment empirically or serve as negative training/test data for regulatory variant prediction methods.

vSampler runs significantly faster than existing tools, supports both SNPs and indels and provides comprehensive state of art variant annotations as matching properties. A novel data structure and algorithm were developed to achieve this performance improvement.

Demo Result

Please input your variant calls (required)

!!! Please make sure your variant calls are tab-delimited or comma-delimited.

Or, upload a variant file

     Upload File
    Click here to get format description
    Set true if the first line of your data is header.
    The choice of population would affect MAF, gene density (when using LD to define variant loci) and number of variants in LD.
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    Advanced options (optional)

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    Other options (optional)

    Please input a number between [1-10000]
    If your inputs are less than 10,000, the max size of annotation number is 1000 If your inputs are less than 100,000, the max size of annotation number is 10, otherwise the max size will be set to 1 If you have more annotation requirements, please download tool and database to run local.

    Please fill in your job information (optional)

    Please fill in E-mail Address to retrieve your job.

    Please cite vSampler as follows:

    Huang D#, Wang Z#, Zhou Y#, Liang Q, Sham PC, Yao H*, Li MJ*. vSampler: fast and annotation-based matched variant sampling tool. Bioinformatics. 2021 Jul 27;37(13):1915-1917.