Ensembl data

Question

[Eliza]

Hi, I used the Ensembl website for SNPs annotation. I uploaded to their website a VCF file with a list of SNPs. Example of SNPs:

#Chrom  Pos Ref Alt 
1   13116   T   G   
1   13118   A   G   
1   16682   G   A   
1   900161  C   G   
1   902288  G   A   
1   980460  G   A   
1   1362903 G   C   
1   1414714 A   G
1   1420704 C   T   
1   1560103 C   T
1   1600156 C   G   

And I got thos files as a result :

The problem is that the result file from the website doesnt have the REF and ALT column so i cant know exactly which SNP it stands for example : 1:13116-13116 is chrom 1 pos 13116 but no information in REF and ALT allele to connect it to my SNP file as there are multiple entries for 1:13116-13116. Is there any way to "fix" this output in Ensembl? is it connected to :"Transcript database to use" on ensembl (https://www.ensembl.org/Homo_sapiens/Tools/VEP?db=core;expand_form=true;tl=YSu3e94WHDBwtREC-8879777) Thank you :)

[Ram]

Do not leave your previous questions unresolved.

Answer 1

[Ram]

You live, you learn. Always add a unique identifier in the input so you can map the output back. I add an ID column with ${CHR}_${POS}_${REF}_${ALT} as the values for this purpose.

Add this column and re-run VEP.

[Eliza]

the problem is that the ID column in my VCF from where I got the SNPs is NA for all SNPs so I identifty SNPs based on CHROM-POR-REF-ALT combination, so is there any other way ?

[Ram]

No, you're going to need to re-run it. Prepare the input before providing it to VEP.

[Ben Moore]

In addition to Ram's suggestion, I'd just like to add that the 'Allele' column in the output is the alternate allele. The reference allele isn't displayed by default in the web based VEP tool but you can use the --show_ref_allele flag when running the command line VEP tool to output the reference allele: https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_show_ref_allele