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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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ERROR: transcript end (1235) for NM_032454.1 is longer than transcript length 444, skipping this transcript #162

Closed asmlgkj closed 3 years ago

asmlgkj commented 3 years ago

Thanks a lot for great tool annovar,can you have a look of this,

asmlgkj commented 3 years ago

Inversion Variant can annovar output MNP as hgvs name synax https://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ like NM_004006.2:c.4145_4160inv <> I add polish and hgvs, but does not work

kaichop commented 3 years ago

The inversion annotation is not supported. Users need to annotate this yourself, for example, checking whether Ref is the reverse complement of Alt, to determine whether the 16bp multi-nucleotide variant is an inversion or not.

On Wed, Oct 6, 2021 at 8:50 AM curry_fan @.***> wrote:

Inversion Variant can annovar output MNP as hgvs name synax https://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ like NM_004006.2:c.4145_4160inv

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asmlgkj commented 3 years ago

thanks a lot ERROR: transcript end (1235) for NM_032454.1 is longer than transcript length 444, skipping this transcript how this happens

kaichop commented 3 years ago

Sometimes there is annotation error for transcript, in this case, the end position is longer than the total length, so annovar considers it as an invalid transcript annotation and skips it.

On Mon, Oct 11, 2021 at 11:47 PM curry_fan @.***> wrote:

thanks a lot ERROR: transcript end (1235) for NM_032454.1 is longer than transcript length 444, skipping this transcript how this happens

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