Cohort Browser geno filters high impact variant with OR

Former User of DNAx Community_30

Dear community,

 

I?m writing with regards to the gene filtering in cohort browser.

 

Once in projects > manage, I select appxxxxxx.dataset and the Cohort Browser opens

Then, I select: Add Filter > GENO > Gene/Effect 

After that, I select: Variant Effect as High Impact 

 

Until this point everything is fine but once arrived here, I encounter some limits.

In particular, I would like to find the samples with high impact variant in at least one of 10 genes. 

 

From the options I see that:

  • I am allowed to insert a maximum of 5 gene names
  • The cohort will be selected using AND but I would like it to be selected using OR

 

Browsing online, I found this resource https://documentation.dnanexus.com/user/cohort-browser and I thought that ?join filter? could have been an option but it seems not to be applicable to the geno filters, only to the pheno ones.

 

Also, I watched some youtube videos about cohort filtering through R studio (https://www.youtube.com/watch?v=iy22sxlj5Ik ) Jupyter (https://www.youtube.com/watch?v=jodNjrYF8po ) but they do not show specific examples for this case.

 

I was wondering if you could please indicate me which is the best way to overcome these limits and retrieve successfully samples with high impact variant in at least one of 10 genes of interest.

 

Thank you in advance for the support,

 

Veronica Erconi

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