kaichop
commented
8 months ago If it is just an insertion at a location, then the start and end needs to be identical to each other. Here you have a 3.2kb genomic region in the file, and this is not an insertion. Clearly this region covers exons.
On Tue, Jan 23, 2024 at 2:03 PM MariosGvr @.***> wrote:
Hi, thank you for the incredible tool!
While reviewing my results table, I noticed that certain insertions marked as exonic actually start in an intronic position. Considering both the start and end positions, these insertions potentially "cover" an exonic region.
However, in my understanding, an insertion that begins in an intron should be classified as intronic, as it "pushes" the exon further away rather than spanning it. Is there a specific notion behind which PhenoSV marks those insertions as exonic?
I'm using the terminal version of the PhenoSV tool for annotating multiple SVs, and the web version gives me the same results.
Example:
chrom start end length svtype Elements Type chr14 39064016 39067194 3178 insertion SEC23A Exonic
Start position on an intronic region: image.png (view on web) https://github.com/WGLab/PhenoSV/assets/101292511/30fc9cb7-2910-45d7-a6ae-e64ab66512ef
Range of SV (Start position marked with the blue line, SV spans on the right): image.png (view on web) https://github.com/WGLab/PhenoSV/assets/101292511/8bd95878-0f32-467e-a78b-bda93ffe2037
Thank you!
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MariosGvr
Hi, thank you for the incredible tool!
While reviewing my results table, I noticed that certain insertions marked as exonic actually start in an intronic position. Considering both the start and end positions, these insertions potentially "cover" an exonic region.
However, in my understanding, an insertion that begins in an intron should be classified as intronic, as it "pushes" the exon further away rather than spanning it. Is there a specific notion behind which PhenoSV marks those insertions as exonic?
I'm using the terminal version of the PhenoSV tool for annotating multiple SVs, and the web version gives me the same results.
Example:
Start position on an intronic region:
Range of SV (Start position marked with the blue line, SV spans on the right):
Thank you!