Hi all,
I installed the VEP (Variant Effect Predictor) Program using Anaconda. and output was obtained without error.
Code I run:
vep -i Final.vcf -gff data.gff.gz -fasta genomic.fna
My output:
Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra
CM009840.1_10757615_A/G CM009840.1:10757615 G 102405271 XM_006078640.2 Transcript missense_variant 639 607 203 T/A Act/Gct - IMPACT=MODERATE;STRAND=1;SOURCE=data.gff.gz
CM009840.1_10757615_A/G CM009840.1:10757615 G 102405271 XM_025278176.1 Transcript missense_variant 639 607 203 T/A Act/Gct - IMPACT=MODERATE;STRAND=1;SOURCE=data.gff.gz
CM009840.1_10757615_A/G CM009840.1:10757615 G 102405271 XM_025278183.1 Transcript missense_variant 639 607 203 T/A Act/Gct - IMPACT=MODERATE;STRAND=1;SOURCE=data.gff.gz
But, the problem is that it did not calculate Sift for me. As a rule, should display the value of Sift in the last column. Given the script executed and the resulting output, I want to know how to get the Sift value for each missense_variant.
Best Regard
Mostafa
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mostafarafiepour
1 answer
As recently indicated in your repost of this question, you are working on the Buffalo genome (Bubalus bubalis). You should have stated this right away, because it is not in the list of current Ensembl genomes. Therefore, it is no surprise that the sift is not calculated, as the annotation for this species does not exist at Ensembl (correct my if I am wrong). I am not well-familiar with SIFT at all, but there are two things you have to do. First, use the correct command line. In your new question, you are again missing the --sift parameter. Second, as annotations are missing at Enselbl, yu have to find out if it is possible to obtain custom sift scores for your species and use them with VEP. I suggest you contact the Ensembl Helpdesk with this problem, providing as much information as you can in your email. I will close the new question of yours, to keep updates focused in this thread here. Please modify the question here by including the information on the species. There is no point in opening multiple questions on the exact same topic. It only spreads information to different threads and potentially annoys users who already contributed with help in the first place.
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Please read the manual. You have to set a flag to tell VEP to output SIFT scores.
many thanks for your reply,
I've implemented the script as follows, but I gave the same output.
Any error or warning messages? What is the output of
Error does not just WARNING.
Sorry I did not understand, what this script is about?
I run this script but again give the same output and do not count the Sift for any missense_variant?
Please do not paste text as screenshots - copy the text as either paste it with code formatting or paste in a github gist and use the link here.