search

WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
218 stars 331 forks source link

Can annovar do structural variants annotations? #197

Open akhilpampana opened 2 years ago

akhilpampana commented 2 years ago

Hello , I am trying to run structural variants annotations using annovar. Do annovar support it? If so can u help me with how to toggle structural variants input so the algorithm can get that?

Regards Akhil

kaichop commented 2 years ago

You can do region-based annotation on structural variants. The input file can be in generic format, chr, start, end, ref, alt are the columns. The ref and alt can be "0" indicating unknown. For translocations, if you have single-base resolution breakpoints, you can treat it as two separate indels to see where the breakpoints are located in annovar.

On Fri, Jul 1, 2022 at 1:08 PM akhilpampana @.***> wrote:

Hello , I am trying to run structural variants annotations using annovar. Do annovar support it? If so can u help me with how to toggle structural variants input so the algorithm can get that?

Regards Akhil

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/197, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OB3GPKWD7T7ST4IUL3VR4QZXANCNFSM52NKBOOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

akhilpampana commented 2 years ago

Thank you so much for the response. I will check and let you know if any questions