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kircherlab / CADD-SV

CADD-SV – a framework to score the effect of structural variants
https://cadd-sv.bihealth.org
MIT License
14 stars 3 forks source link

Input format #1

Closed alhafidzhamdan closed 3 years ago

alhafidzhamdan commented 3 years ago

Hi there, Thanks for creating this tool! I'm trying to use your website form to annotate my SV bed file. It's not clear how one should structure the format of the input bed file however. Given a bedpe format file, which coordinate of the pair goes to column 2 and 3?

Here's mine (here i've taken the end2 as column 3).

head id_C3N-03182T.bed 
chr2    190386065   190386151   DEL
chr2    190386111   190386105   DEL
chr4    131591037   131591084   DEL
chr4    131591082   131591039   DEL
chr5    38553621    38553674    DEL
chr5    38553658    38553637    DEL
chr5    180507818   180508071   DUP
chr5    180508068   180507821   DUP
chr8    111256766   111256830   DUP
chr8    111256827   111256769   DUP

I'm not getting any output whatsoever from the website.

Also am I right in thinking the tool does not include inversion and translocation? A

makirc commented 3 years ago

Hi there, Thank you for your message and interest in the software.

Your input format looks good. If the website is not rejecting an uploaded file than the basic format is correct. Files are parsed before saving on our server for further processing. Must be a problem on our end with the processing. I see that you got an empty file back. I also see a problem, you are using coordinate ranges that start before they end: chr12 68522146 67227031 Unfortunately, this is currently not correctly handled by our pipeline and the complete file is rejected. I just inserted a check that will switch start and end in the upload. Please reupload your file. Sorry for the inconvenience.

You are also correct in that we are not supporting inversions or translocations (we did not have training data for these kinds of events).

Best, Martin

alhafidzhamdan commented 3 years ago

Hi Martin, Thanks for getting back and tweaking your code, it seems to work now. A