Question: (Closed) Annotation with VEP for genome Buffalo (Bubalus bubalis).
0
gravatar for mostafarafiepour
19 months ago by
mostafarafiepour70 wrote:

Hi All,

I want to explore here with the help of all friends a good way to make the buffalo genome annotation using VEP.

As you all know, the reference of Buffalo genome and annotation file it (gff3), was recently released at the chromosome level (Almost four months ago). So, the buffalo genome in the VEP database has not cache. Now we only have a genome reference and an annotation file (gff3) with a VCF file for annotation.

It is noteworthy that, previously, I tried to run VEP using Anaconda and i got the output without error. But my output file is incomplete.

Code i run:

grep -v "#" GCA_003121395.1_ASM312139v1_genomic.gff | sort -k1,1 -k4,4n -k5,5n -t$'\t' | bgzip -c > data.gff.gz
tabix -p gff data.gff.gz
vep -i Final.vcf -gff data.gff.gz -fasta genomic.fna

and 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 I 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

snp vep • 501 views
ADD COMMENTlink written 19 months ago by mostafarafiepour70

sift and polyphen (and condel) are theoretical clinical significance predictions. I am not sure if they apply to non-human samples. But this post here says you can : Running Sift And Polyphen In Mouse And Other Species

ADD REPLYlink modified 19 months ago • written 19 months ago by cpad011213k

Did you follow ATPoint's suggestion from your other thread?

ADD REPLYlink written 19 months ago by RamRS27k

Hello mostafarafiepour!

This is a duplicate post of 346279. I commented on your matter in the first question and gave suggestions how to proceed, closing this one to keep things focused in one thread.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 19 months ago • written 19 months ago by ATpoint36k
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