Deletions together with SNVs on BAM files

Question

[baliczap]

Dear All, I frequently see such variant on genome browser when looking at variants. I was wondering what is the source of this? It seems as it would be a haplotype, but quality is frequently low by variants such as this. I thought on pseudogene effect, but could not prove so. Any idea? Thank you

[desouzareis.r]

Hi,

These kind of variants are usually called delins and there are some pathogenic known delins variants. In this article there are some suggestions of possible causes of such mutations:

It has been suggested that the hypermutability of CpG dinucleotides could be thecause of these complex mutations ... The rich CpG sequences are not the only hotspot regions with a high degree of mutability. Overrepresentation of some penta-, tetra-, and trinucleotide motifs in the vicinity of delins has been described...