Amino acid change from vcf
I am trying to add in the amino acid change caused by the SNPs in my VCF file using R. I have no idea how to go about this. I have successfully added in the gene name and have the protein fasta of the genome (H37Rv). I have found a website that does this but would like to incorporate it into my pipeline (http://www.platform.genexplain.com/procannot/index.php?action=annotation).
I tried using ensemble VEP but could not get it to work, even using the online version. I too tried SIFT 4G which gave incorrect results.
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hello, you must add the point mutation in the sequence or protein structure?or what?just to understand well your question
hi, I have my vcf with my snps in it and I just want to know what amino acid change each snp causes. I assume I can somehow use the fastq file from the genome to do this but not sure how. would be great if I could get a premade tool like VEP to work
Not really. This involves finding the start codon and figuring out the contextual meaning of the nucleotide change and then translating the codon change to amino acid change.
And "get XYZ to work" is really a weird way to ask for help. You should ideally state what you've tried, the exact problem you're facing along with any error message if applicable. The more detail you give, the better chances you have of getting help from folks here.
Using VEP or snpEff would be the normal route. If you couldn't get VEP to work, then just say what didn't work and we can help with that.
hi, the problem I'm having with VEP is that it returns no annotations on my file. I used the online tool and uploaded my vcf and selected the m. Tb h37Rv genome that I used for my variant calling.
You might wanna edit your question and add this content in there.