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 :)
1 answer
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
Log in to answer this question.
-
convert tsv file to VCF
written by Eliza •
-
Tutorial: Converting TSV file to VCF
written by barslmn •
-
Variant Effect Predictor For Two Individuals Output
written by Houkto •
Do not leave your previous questions unresolved.