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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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frameshift insertion HGVS different protein position between Annovar and VEP #211

Open RysBen opened 1 year ago

RysBen commented 1 year ago

Hi there,

I found an issue which is similar to #54. Specificlly, A insertion variant has different HGVS description(position) between Annovar and VEP.

Version: 2016-02-01

Comand:

perl table_annovar.pl test.vcf -vcfinput human_db/ -buildver hg19 -remove -protocol refGene -operation g -arg '--splicing_threshold 10 --exonicsplicing' -nastring . -out ./ --outfile out

This insertion variant is as below:

chr13 32937354 . T TA

Annovar Result: image BRCA2:NM_000059:exon18:c.8016dupA:p.I2672fs

VEP online Result: image NP_000050.3:p.Ile2675AspfsTer6

What causes this difference of protein HGVS? Which one is correct?

kaichop commented 1 year ago

can you try add -polish argument and see what is the result? I plan to make it a default option because too many people do not use it and this has caused problems for some indels. My results using ANNOVAR shows I2675Dfs*6

On Wed, Feb 15, 2023 at 9:46 PM Shuaibing @.***> wrote:

Hi there,

I found an issue which is similar to #54 https://github.com/WGLab/doc-ANNOVAR/issues/54. Specificlly, A insertion variant has different HGVS description(position) between Annovar and VEP.

Version: 2016-02-01

Comand:

perl table_annovar.pl test.vcf -vcfinput human_db/ -buildver hg19 -remove -protocol refGene -operation g -arg '--splicing_threshold 10 --exonicsplicing' -nastring . -out ./ --outfile out

This insertion variant is as below:

chr13 32937354 . T TA

Annovar Result: [image: image] https://user-images.githubusercontent.com/36749963/219254880-5d738c27-2cad-4ccf-bc52-9b3f1d680e3e.png BRCA2:NM_000059:exon18:c.8016dupA:p.I2672fs

VEP online Result: [image: image] https://user-images.githubusercontent.com/36749963/219253584-10d28f32-2a6b-49cd-bc0e-3ae7dd7bf9fa.png NP_000050.3:p.Ile2675AspfsTer6

What causes this difference of protein HGVS? Which one is correct?

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RysBen commented 1 year ago

Thank you, kaichop.

Based on your suggestion, I tried a newer version (because I could't find -polish in the 20160201 version), and it workers for protein position. When I used right normalization, cDNA's position was also same with results from VEP online.

image