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CoVaCS: Consensus Variant Calling System

Help

1. Study creation

Click on the "new submission" button from the homepage. Click on the create a new study button. Enter a name and a description for the new study.

2. Add files

You will be redirected to the upload page. Click the add files button and select the input files from your computer.

3. Upload files

Click on the start upload button and wait for the upload to be finished. Then, click on the Continue button.

4. Assign files

If your files are produced by a paired-end sequencer, assign those files to the same box. When you're done, click on the Continue button.

5. Complete metadata

Then, it's required to enter a descriptive tags for each of your files (such as which kind of tissue/organism has been sequenced ). When this step is finished, you can click on the Continue button and return to your study page.

6. Create analysis

Click on the button "New analysis with selected file(s)". By clicking on "Choose a pipeline" menu you can define which kind of analysis you wish to run (Single Sample or Joint Samples Procedure) and which read aligner you prefer between BWA and Bowtie2.

7. Define analysis Parameters

The last step is to tune some of the parameters for your analysis such as the reference genome and the enrichment kit in case of WES and Target Exome Sequencing analysis. We selected the most suitable parameters for each step of the pipeline. (If you need additional information, you can read our FAQ).

8. Start!

When you're ended all the previous steps, click on the Start analysis button.

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