Closed methionine23 closed 1 month ago
Please detail your request when reporting a bug:
Thanks! I made an artificial variant and tested it on the web server. The full mode has frameshift filed empty, while split mode predicted yes. I didn't find an explanation in the documentation as I may have missed it. https://lbgi.fr/AnnotSV/result?id=qo71GNbvUi https://lbgi.fr/AnnotSV/result?id=dWCiPEsbcN Also I run v.3.4.2 using bed file, the split mode returned 2 rows, while the web server only returned one row for split mode. Maybe that is expected?
The full mode has frameshift filed empty, while split mode predicted yes.
Ok, got it.
In the README, you can see in the "Annotation columns available in the output file" section:
As you can see, the frameshift
is never filed for the "Full" lines.
Why?
You need to understand the full and split lines.
For each gene, only a single transcript from all transcripts available for this gene is reported in the following order of preference:
To resume, the frameshift
value depends on the transcript of 1 gene.
Full and split lines:
Considering the “full” length annotation of one SV, AnnotSV does not report the Gene-based annotation (value is set to empty), except for scores and percentages where AnnotSV reports the most pathogenic score or the maximal percentage.
I hope this helps you understand better, Best,
Véronique
Also I run v.3.4.2 using bed file, the split mode returned 2 rows, while the web server only returned one row for split mode. Maybe that is expected?
The results are exactly the same between your local run (1 full line + 1 split line) and the web server.
It seems that you have selected the "COMPACT" mode in knotAnnotSV (web server) which only displays full lines.
cf https://github.com/mobidic/knotAnnotSV:
Thank you for the detailed information!
Hello, I found that some CNV calls involving two genes had different result between full vs split mode. Full mode returned NaN, while one of the split call predicted frameshift correctly. Is this behavior by design? Thank you!