Question: Get Flanking Amino Acid Sequence
gravatar for windsur
11 weeks ago by
windsur10 wrote:

Dear all,

I've just perform an exome-seq and I've obtained the vcf file. Now to continue with my experiment, I need to extract the flanking regions wt and mut type of my dataset because I need to synthesize that for an immunotherapy research. I mean, in my vfc file I have a column like this:



And the desire output is like this:

Wt Epitope                  Mut Epitope

In case I've more than one transcritp, I'll need the first one. I know how to obtain the the flanking regions of nucleotides, but I had not find anything similar like a refGene.txt of amino acids. I've used hg19 as genome reference.

Any help is welcome!

python snp sequence dna-seq R • 158 views
ADD COMMENTlink modified 10 weeks ago • written 11 weeks ago by windsur10

Thank you Chris! But unfortunately I do not have a lot of time to learn how to use pVACtools, because I will need to use another format of my vcf file... I think there is another way faster to do what I need. Because if we have to amino acid position (e.g. G580C), with a script similar of bedtools I could get the flanking position. if anyone can help I will be very happy :)

ADD REPLYlink written 10 weeks ago by windsur10
gravatar for Chris Miller
11 weeks ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

Highly suggest that you check out the pVACtools suite, which utilizes some VEP plugins and custom parsing to extract exactly this information and format it nicely prior to doing binding affinity predictions.

ADD COMMENTlink written 11 weeks ago by Chris Miller20k
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