You are getting this error because there were no variants found in your analysis. This could be from a variety of causes: (1) you actually have no variants in your sample, (2) the parameters you are using are too stringent, or (3) there could be a sample quality issue. Below are some potential solutions you could explore:
Solution 1 - Use less stringent parameters
You can change the parameters under the "Change default options" section when you are setting up the analysis. Here are some parameters you might consider:
- Minimum depth of coverage to call variants.
- Minimum base quality and mapping quality. Though we do not recommend you set these to something lower than 10.
While Basepair tries to use reasonable default parameters, they will not work for all samples. How to optimize variant calling parameters can depend on many things like sample collection method (e.g. flash frozen vs formalin-fixed), tissue type, type of sequencing machine, and others.
Solution 2 - Checkout the quality of your samples
Our first suggestion is to check the alignment results for your samples. Here are some things you could check:
- The quality of most bases in the sequencing reads should be above 30.
- Most of your reads should be uniquely aligned.
- The average depth of coverage should be around what you specified when you were configuring how to sequence your samples.
Solution 3 - Contact us
Contact us by either:
- Creating a ticket here: http://support.basepairtech.com/support/tickets/new
- Message us using the chat icon in the lower right corner of your screen on the Basepair dashboard.