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Sequencing assay selection

When launching a new analysis without workflows, you will be prompted to select a “DNA and/or RNA Assay” (depending on the analysis type). This refers to the capture or amplicon kit used to sequence your sample.

Selecting an assay is mandatory for DNA analyses initiated from FASTQ files, as well as for RNA and DNA+RNA analyses, because it defines the target regions used for alignment and variant calling.
For analyses initiated from VCF files, selecting an assay is optional, since the assay information is not used during variant annotation.

Example: DNA analysis from FASTQ files

Example: DNA+RNA analysis from FASTQ and TSV/CSV

 

Your assay is not in the list? 

If your assay is not listed, you can request us to add it by navigating to Help > New Assay Request and filling all the required details before submitting the request. 

You can find more information in the following two documents:

 

What is the assay information used for?

The assay defines the genomic coordinates targeted during sequencing. This information is especially relevant  when launching an analysis from FASTQ generated by a sequencing experiment that is not whole-exome or whole-genome (e.g. a gene panel). In these cases, variant calling is performed in targeted mode, meaning VarSome Clinical will only call variants within the assay’s defined regions. 

Additionally, assay’s information is used to calculate alignment statistics and coverage of the targeted regions. The statistics are used to generate the QC report.