Alternative allele in VEP output

Question

[zizigolu]

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

Answer 1

[Ben_Ensembl]

Hi A,

The 'Allele' field in the VEP output is the alternative allele that is supplied in the input and that has been used to calculate the consequences for that output row.

More information about the output fields can be found in the documentation: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#output

Best wishes

Ben Ensembl Helpdesk

[zizigolu]

Thank you, so if I need both alternative and wild alleles in one file I should add the wild allele manually?

[Ben_Ensembl]

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

[zizigolu]

Thank you

I have annotated my .vcf by web VEP and this is output.vep

head(my_VEP)
#Uploaded_variation Location    Allele  Gene    Feature Feature_type    Consequence cDNA_position   CDS_position    Protein_position    Amino_acids Codons  Existing_variation  Extra
.   1:782112-782112 A   ENSG00000237491 ENST00000412115.2   Transcript  intron_variant,non_coding_transcript_variant    -   -   -   -   -   -   IMPACT=MODIFIER;SYMBOL=LINC01409;BIOTYPE=lncRNA;INTRON=1/4;STRAND=1;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC:50701;TSL=3
.   1:782112-782112 A   ENSG00000237491 ENST00000429505.6   Transcript  intron_variant,non_coding_transcript_variant    -   -   -   -   -   -   IMPACT=MODIFIER;SYMBOL=LINC01409;BIOTYPE=lncRNA;INTRON=1/3;STRAND=1;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC:50701;TSL=3

For an algorithm I need such VEP output

> head(VEP_downloaded_from_paper[1:2,])
                                      V2            V3 V4      V5 V6 V7
1 LP2000104-DNA_A01_vs_LP2000101-DNA_A01 1_1040124_C/T  1 1040124  C  T
2 LP2000104-DNA_A01_vs_LP2000101-DNA_A01 1_1040124_C/T  1 1040124  C  T
               V8                                          V11
1 ENSG00000131591        intron_variant,NMD_transcript_variant
2 ENSG00000131591 intron_variant,non_coding_transcript_variant
                                                                                                                                                                                                                         V18
1 STRAND=-1;SYMBOL=C1orf159;SYMBOL_SOURCE=HGNC;HGNC_ID=26062;BIOTYPE=nonsense_mediated_decay;ENSP=ENSP00000463144;TREMBL=J3QKM1_HUMAN,B2REC5_HUMAN;UNIPARC=UPI0000205ACB;INTRON=1/11;HGVSc=ENST00000467751.1:c.-136+11316N>A
2                                                                                        STRAND=-1;SYMBOL=C1orf159;SYMBOL_SOURCE=HGNC;HGNC_ID=26062;BIOTYPE=retained_intron;INTRON=1/2;HGVSc=ENST00000472741.1:n.28+11316N>A
  GMAF propGMAP     gene
1    0        0 C1orf159
2    0        0 C1orf159
>

As you are seeing, in the second VEP output there are two extra columns GMAF and propGMAP

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

[Kevin Blighe]

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

[zizigolu]

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

[Kevin Blighe]

Please ask Maria for the exact command that she used, and the version of VEP.