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Run InterVar on pre-annotated VCF (annotated using a different tool) #91

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nidhih2 opened this issue May 15, 2023 · 1 comment
Open

Run InterVar on pre-annotated VCF (annotated using a different tool) #91

nidhih2 opened this issue May 15, 2023 · 1 comment

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@nidhih2
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nidhih2 commented May 15, 2023 •
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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!
@nidhih2 nidhih2 changed the title Run InterVar on already annotated VCF using a different annotating tool Run InterVar on pre-annotated VCF (annotated using a different tool) May 15, 2023
@zgtman
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zgtman commented Aug 17, 2023

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

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@zgtman @nidhih2