Identifying samples containing a given variant in VarSome Clinical

How can I identify which of my samples contain a given variant?

VarSome Clinical allows you to search for any of your analyzed samples in which a variant has been found. To illustrate this feature, we will show you how to identify all the samples containing the variant chr7:140453136:A:T.

First, go to the “Samples” page, type the variant you are looking for and press enter/click on search (🔍):

Only those samples containing the variant will be shown in the “Samples” menu.

Can I find a specific variant in a subset of samples?

It is also possible to identify samples containing the given variant within a subset of analyzed samples. To do this, you can combine the previous feature with the Sample Tags feature. 

First, you will need to label the samples of interest using the Sample Tags. Then, you can go to the “Samples” menu and search for a specific variant in a subset of samples labeled with a particular Tag.

In the example shown in the picture below, we have identified the variant chr7:140453136:A:T among all the samples labeled with the tag “sampletag”.

Accepted formats for variant search queries

You will be able to identify samples containing the given variant using different variant annotation formats:

  • Chromosome - position - ref seq - variant seq (e.g. chr7:140453136:A:T)
  • HGVS DNA-level variants (e.g. BRAF:c.1799T>A, BRAF(NM_004333.6):c.1799T>A)
  • HGVS single amino acid substitutions (e.g. BRAF Val600Glu, BRAF p.Val600Glu, BRAF V600E)
  • dbSNP rs id (e.g. rs113488022)