<p>I'm working on rather standard whole-exome sequencing data and treat it the same as whole-genome sequencing data (aligning it to the full GRCh38 reference assembly and calling variants with no exome-related parameters).</p>

<p>I recently noticed that my variant calling results contain numerous variants mapped to a non-exomic region, incidentally, some of them were significantly associated with the phenotype I study.</p>

<p>My questions are as follows:</p>

<ol>
<li>Are the non-exome variants in my exome data invalid? or could it be that the exome kit captured more than it was designed to capture?</li>
<li>Should I treat raw exome sequencing data any different than genome sequencing data, and if so, what parts of my pipeline should be modified to accommodate exome data?</li>
</ol>

<phylogenetics><variant-calling><exome>
Non-exome variants called from whole-exome sequencing data
# Non-exome variants called from whole-exome sequencing data

(Asked by: username_0 on 2020-06-14)

I'm working on rather standard whole-exome sequencing data and treat it the same as whole-genome sequencing data (aligning it to the full GRCh38 reference assembly and calling variants with no exome-related parameters).

I recently noticed that my variant calling results contain numerous variants mapped to a non-exomic region, incidentally, some of them were significantly associated with the phenotype I study.

My questions are as follows:

1. Are the non-exome variants in my exome data invalid? or could it be that the exome kit captured more than it was designed to capture?
2. Should I treat raw exome sequencing data any different than genome sequencing data, and if so, what parts of my pipeline should be modified to accommodate exome data?

**Tags:** phylogenetics, variant-calling, exome

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## 0 answers

