[ensembl-dev] VEP vcf annotation

[Dietmar Rieder]

Thanks Diana,

I completely missed that, it makes of course sense, sorry for the noise.

Best
   Dietmar

On 7/2/21 1:01 PM, Diana Lemos wrote:
> Thanks for sharing the command.
> 
> Your commands are not the same, to generate the VCF output you have the 
> option --pick which is going to pick one consequence per variant 
> according to the criteria described here: 
> https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick 
> <https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick>
> 
> This option is not being used in your second command. If you remove 
> --pick you should have the same number of consequences in both outputs.
> 
> 
> Best wishes,
> 
> Diana
> 
> 
> On 02/07/2021 11:45, Dietmar Rieder wrote:
>> Hi,
>>
>> here is the command for the vcf output:
>>
>> vep -i CRC15_CRC15_normal_Somatic.hc.vcf.gz \
>>     -o CRC15_CRC15_normal_tumor_vep.vcf \
>>     --fork 16 \
>>     --stats_file CRC15_CRC15_normal_tumor_vep_summary.html \
>>     --species homo_sapiens \
>>     --assembly GRCh38 \
>>     --offline \
>>     --cache \
>>     --cache_version 103 \
>>     --dir /data/databases/vep_cache \
>>     --dir_cache /data/databases/databases/vep_cache \
>>     --hgvs \
>>     --fasta 
>> /data/databases/vep_cache/homo_sapiens/103_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz 
>> \
>>     --pick --plugin Frameshift --plugin Wildtype \
>>     --plugin 
>> ProteinSeqs,CRC15_CRC15_normal_tumor_reference.fa,CRC15_CRC15_normal_tumor_mutated.fa 
>> \
>>     --symbol --terms SO --transcript_version --tsl \
>>     --vcf 2> vep_errors_1.txt
>>
>>
>>
>> and this is the command for the table output:
>>
>> vep -i CRC15_CRC15_normal_Somatic.hc.vcf.gz \
>>     -o CRC15_CRC15_normal_hc_vep.txt \
>>     --fork 16 \
>>     --stats_file CRC15_CRC15_normal_hc_vep_summary.html \
>>     --species homo_sapiens \
>>     --assembly GRCh38 \
>>     --offline \
>>     --dir /data/databases/vep_cache \
>>     --cache \
>>     --cache_version 103 \
>>     --dir_cache /data/databases/vep_cache \
>>     --fasta 
>> /data/databases/vep_cache/homo_sapiens/103_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz 
>> \
>>     --format "vcf" \
>>     --everything \
>>     --tab 2> vep_errors.txt
>>
>> Best
>>    Dietmar
>>
>> On 7/2/21 12:18 PM, Diana Lemos wrote:
>>> Hi Dietmar,
>>>
>>> I'm unable to reproduce the issue. Could you please send me the VEP 
>>> command you are running?
>>>
>>>
>>> Thanks
>>>
>>> Diana
>>>
>>>
>>> On 02/07/2021 10:52, Dietmar Rieder wrote:
>>>> Hi,
>>>>
>>>> we are using VEP (103) to annotat our VCFs and we just stumbled over 
>>>> the situation that for the mutation chr5_112838250_C/T 
>>>> (chr5:112838250) we get 7 annotated transcript variants in the gene 
>>>> with SYMBOL ACP and one in the "gene" with SYMBOL AC008575.1, in the 
>>>> VEP txt output, which is fine.
>>>>
>>>> BUT
>>>>
>>>> when we use -vcf to get an annotated vcf file we get the mutation on 
>>>> that position only annotated with the SYMBOL AC008575.1
>>>> This is problematic, because the canonical gene here is APC (a known 
>>>> driver gene in CRC) and we miss it when parsing the VCF
>>>>
>>>> Would it be possible to add all gene symbols to the SYMBOL field in 
>>>> the CSQ of the vcf?
>>>>
>>>> Thanks
>>>>   Dietmar
>>>>
>>>>
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>>
>>


-- 
_________________________________________
D i e t m a r  R i e d e r, Mag.Dr.
Head of HPC/Bioinformatics facility
Innsbruck Medical University
Biocenter - Institute of Bioinformatics
Innrain 80, 6020 Innsbruck
Phone: +43 512 9003 71402
Fax: +43 512 9003 73100
Email: dietmar.rieder at i-med.ac.at
Web:   http://www.icbi.at


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