Tutorial Burden test

Francisco García edited this page Jan 30, 2015 · 3 revisions
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INPUT


STEPS

1. Select your data
2. Select regions of interest
3. Choose statistical parameters
4. Fill information job
5. Press Launch job button


OUTPUT





INPUT

Input data
  • Input data should be a zip file contains the PED and VCF files. See data types here.

  • PED files contain genotype information (one person per row).

  • Babelomics can read .zip, .gz and .tar.gz files but needs to be able to uncompressed data without finding any folder structure.


STEPS

Select your data

First step is to select your data to analyze.

Select regions
  • Choose the Human genome version: GRCh37 or GRCh38.
  • Select the query region: All protein coding genes or a custom region.
Choose statistical parameters
  • Rare allele frequency threshold

  • p-value

  • Number of permutarions. 100 permutations by default.

Fill information job
  • Select the output folder
  • Choose a job name
  • Specify a description for the job if desired.
Press Launch job button

Press launch button and wait until the results is finished. A normal job may last approximately few minutes but the time may vary depending on the size of data. See the state of your job by clicking the jobs button in the top right at the panel menu. A box will appear at the right of the web browser with all your jobs. When the analysis is finished, you will see the label "Ready". Then, click on it and you will be redirected to the results page.


OUTPUT

Input parameters

In this section you will find a reminder of the parameters or settings you have used to run the analysis.

Output files

  • Here you will find the result generated by the association tool, plain-text and space-delimited data files.

  • Manhattan plot is used to display results along of all regions.



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