AnnotSV structural variant chromosome start/stop position does not match VCF file position

[mxiong2]

Hello,

Is there an explanation why AnnotSV is annotating the start and end position of SV slightly off. I checked the position of the annotated SV against the position in my VCF file but saw that the SV were off. I am annotating the data with the annotation split mode.

Thanks.

[lgmgeo]

Hi,

By default, the includeCI option is set to "1":

-includeCI: To expand the "start" and "end" SV positions with the VCF confidence intervals (CIPOS, CIEND) around the breakpoints
            Values: 1 (default) or 0

To keep the start and end positions, please set the includeCI option to "0".

Best, Véronique

[lgmgeo]

Any news?