When launching a new analysis you are asked to select the "Assay", i.e. the capture or amplicon kit used for sequencing your sample.
What is the assay information used for?
The assay defines the genomic coordinates that are being targeted for sequencing. This is relevant information, especially when you are launching an analysis from FASTQ and your data comes from a sequencing experiment that is neither a whole-exome nor a whole-genome (e.g. a gene panel). In such cases, variant calling will be performed in targeted mode, meaning that VarSome Clinical will only call variants in the regions defined by the assay.
In addition, the assay's information will be used to calculate alignment statistics and coverage of the targeted regions. The statistics are used to generate the QC report.
What should I do if...
I am a VarSome Clinical customer and my assay is not in the list.
Please, visit Adding an assay to VarSome Clinical to find out how you can add your assay to our platform.
- I am using VarSome Clinical, but I am not a customer yet.
We only add custom assays for VarSome Clinical users. If you are in a free trial period, you can select one of our generic options. Don't be afraid of losing information in your results. As mentioned, we only use the assay's information to generate alignment statistics for the QC report. If you finally decide to join us, we will be happy to import your assay to our platform. Refer here for more details.
- I don't know what sequencing kit was used to prepare the capture/amplicon library.
We use the assay's information to generate the QC report. If you don't know or you are not sure which assay was used to sequence your samples, this is not a problem at all. You can select one of our generic options "generic amplicon kit" or "generic capture kit". Just be sure to select the appropriate option for your assay's chemistry (see the next section).
Using one of these options, the variant calling will be performed in untargeted mode, and the alignment statistics (given by the QC report) will not include the "on target" percentage of mapped reads since we will not know what the targeted regions are.
Which generic assay should I use?
When using the generic assays (Generic capture or amplicon kit), your selection must be in line with the chemistry of your sequencing assay. This choice is important because it affects:
- The way we handle possible PCR duplicates.
- The default thresholds set for minimum coverage needed to call a variant. For samples sequenced using an amplicon kit, since such kits tend to have very high coverage, the minimum threshold coverage is higher than for the capture kits.
Please, make sure to choose "generic amplicon kit" for cases where you have sequenced your sample with an amplicon kit and "generic capture kit" for cases where you have sequenced your sample using hybridization capture technology.
Please, note that the samples analyzed using one of the "Generic" kits can not be used for CNV sub-analyses.