Transposable Element Insertions

[Rebeca Borges]

Hi, 

I am required to validate my variants here for submission to a journal. However, there are currently a few issues with the types of variants I am trying to validate that I think Mutalyzer does not support. 

These are transposable element insertions with a target site duplication surrounding the insertion. We have a size estimate of the insertions, but these are not precise, and the sequences cannot be accurately determined with our sequencing technology used. I'm using the HSGV recommendations from: https://varnomen.hgvs.org/recommendations/DNA/variant/complex/ (see L1 example for insdup) as well as the parenthesis that they recommend for uncertain insertion sizes and unknown sequences.

In the example given: NC_000001.11:g.114750025_114750040dupins(267) we have an hg38 insertion of around 267bp with an unknown sequence and a target site duplication. The breakpoints of the insertion and the regions being duplicated are in chr1, breakpoint start 114750025 and end 114750040

The journal will not accept our manuscript until we have an excel file validating these variants, so I really appreciate your help figuring out how we can validate these. Thank you! 

Rebeca