Entering edit mode
4.6 years ago
zizigolu
★
4.3k
Hi
I have annotated a vcd file by online VEP
I am trying were the alternative allele is in the vet output
> head(VEP)
#Uploaded_variation Location Allele Gene Feature
1: . 1:782112-782112 A ENSG00000237491 ENST00000412115.2
2: . 1:782112-782112 A ENSG00000237491 ENST00000429505.6
3: . 1:782112-782112 A ENSG00000237491 ENST00000434264.6
4: . 1:782112-782112 A ENSG00000237491 ENST00000443772.2
5: . 1:782112-782112 A ENSG00000237491 ENST00000457084.1
6: . 1:782112-782112 A ENSG00000228327 ENST00000506640.2
Allele column is for wild or mutant allele ? If wild, where the alternative allele is?
Thanks in advance
Thank you, so if I need both alternative and wild alleles in one file I should add the wild allele manually?
No problem- you can use the --show_ref_allele option if you are running the command line version of VEP: http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#basic
Thank you
I have annotated my .vcf by web VEP and this is output.vep
For an algorithm I need such VEP output
As you are seeing, in the second VEP output there are two extra columns
GMAF
andpropGMAP
Please, do you know what these columns are?
Also in my VEP out put I have 14 columns while likely in second VEP have been more columns
Can you help me please?
My goal is achieving something like the second VEP
Thank you in advance
GMAF is Global Minor Allele Frequency. I have no idea to what 'propGMAP' relates - can you share the source of this second output?
To get what you need, please explore all VEP options that are listed here for you: https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html
Thank you
In this link there is a sample data and script to calculate recombinant homologous deficiency from SNVs
https://bitbucket.org/msecrier/analysisscripts.secrier_etal.natgen2013/src/master/DDR.scripts/sampleData/
I don't know from where Maria has obtained such a VEP because VEP did not give me anything like this
In her paper she mentioned she has used VEP but why VEP does not give the same, I don't have any idea
Please ask Maria for the exact command that she used, and the version of VEP.