Soft and Hard Clipping issue - abnormal IGV profile

Question

[photo.dm77]

Dear all,

we have performed a targeted DNA-seq sequencing using a custom SureSelect XT capture (and a tagmentation-based library). We have used this capture on several samples (more than 200) and we observed an abnormal profile only once in a sample. The reads, soft and hard clipped, are mapped on the exons boundaries of the SLC6A8 gene.

Do you know what can cause this aberrant mapping only in this patient?

I'm attaching an IGV screenshot with two samples, the first with the aberrant profile and the latter without

IGV screenshot:

Answer 1

[trausch]

Looks like a processed pseudogene of SLC6A8 in that patient (gene retrocopy insertion polymorphism).

[photo.dm77]

Interesting observation. Thank you for the reply. Indeed, the SLC6A8 gene has a pseudogene named SLC6A10P. We will further investigate this hypothesis.