Run InterVar on pre-annotated VCF (annotated using a different tool)

[nidhih2]

How do I run this tool on an pre-annotated VCF? The annotation was done with a different tool and not ANNOVAR. I set the parameter "skip_annovar" to TRUE, however, I end up getting

ERROR: The InterVar did not find the annotation result file from ANNOVAR!
ERROR: The name of annotation result file should be like .... 

Thank you!

[zgtman]

Is there any update? I would like to use pre-annotated file also from Annovar, but InterVar has only input options VCF, AVinput and VCF_m.

So I truly believe that you can not use pre-annotated file.

best,

Petr

[alkaZeltser]

For future users, I have found the solution:
Skipping annovar causes InterVar to search for an existing annotated file in the same location where Intervar would have written the multianno file if annovar was not skipped. To facilitate this, make sure the outfile param in your config is pointing to your pre-annotated annovar multianno file.

e.g.

In the config:

outfile = /path/to/annotated/annovar/file/example
# actual file path: /path/to/annotated/annovar/file/example_mulitanno.txt

Run InterVar with skipped annovar:

./Intervar.py -c /path/to/config.config --skip_annovar