automatic analysis of mis/non sens genes

[Jane M]

Hello,

I am wondering if tools for automatic analyses of snps and indels detection have been developped.
Let me explain my problem: I have the results of a DNA-seq experiment. I have a list of SNPs and indels.

For each mis/non sens (stop codon, synonymous mutation...), I would like to know the complete name of the gene, its functions and if the mutation takes place in a "preserved domain" in order to study the consequences of this mutation.

Now, I have to look "by hand" through different websites to find this information (pubmed...). This approach is possible with a small number of such genes. Since I will got an important number of genes to analyze, I would like to find an automatic way for getting these information.

Has anyone heard about such a tool ? Otherwise, I will try to code something with R, but if it already exists, I will same time !

Thanks,
Jane

[Boel]

Hi Jane,

I'm using SnpEff (http://snpeff.sourceforge.net/) which is fast and seems to work well. There are other tools as well, such as ANNOVAR and others.

[Jane M]

Thanks for your answer Boel. Thanks to these references, I've found another one: ensembl effect predictor. I've seen also oncatator, but I haven't found information about it and it might be interesting for me since I'm working in cancer field. Does anyone know this tool ?
If you know other tools, please let me know.

I've seen that there is a web interface to use it. I would like to test it first, but I've some trouble with the input to provide: a tab delimited format, with 5 columns:
- name or number of the chromosome
- start (of the chromosome, insert, snp ?)
- end (of the chromosome, insert, snp ?)
- allele - pair of alleles separated by a '/', with the reference allele first
- strand

What are precisely the start and the end?

Thanks,
Jane

[Boel]

I am unable to find any information about a tool called oncatator, so I am afraid I can not help you.

[Jane M]

It's my mistake, it's oncotator

[swbarnes2]

Annovar is another one that get mentioned frequently. It won't know domains, but it will tell you what gene your mutation is in, and if its an amino acid changing mutation.

I would guess that "start" and "stop" for ensemble do mean the start and stop of the mutation. It's probably written that way to accomodate mutations that aren't simple singel nucleotide changes.

[Jane M]

Thanks for your answer. It seems that it was the start and the end of the mutation, so I'm more or less able to run ensembl effect predictor.
For now, I can only try softwares through a web interface. Do you know other tools that offer this possibility?

I foresee to test annovar later.