Exome Sequencing

Question

[Liyf]

Hi, I have a question, how can I cluster the exome sequencing data to non-synonymy and synonymy and so on? I can not find perl scrip in the internet. But someone tells me that there are many.

Answer 1

[User 59]

I don't know what you mean by 'clustering' but you might want to look at the Variant Effect Predictor from Ensembl:

Web page

API

Perl script

Documentation

[Liyf]

What I want to do is just annotation the mutations in batches. Someone tells me that there are many perl script, but I did not find any. Because I am new, I am not familiar with many website.

Answer 2

[Madelaine Gogol]

Check out snpeff?

[Liyf]

Thanks. I think it is very fit for me. I think I should have a try.

[Liyf]

Excuse me. But I really do not know how to use this soft. I am new. Could you give me an example?

[Madelaine Gogol]

Did you get it installed okay? When I was using it, I was using pombe and had to create my own genome, then the command I had to run was kind of long, something like:

java -jar /path/to/snpEff.jar -config /path/to/snpEff.config -no-downstream -no-upstream pombe_Oct2010 data.vcf > snpeff.txt

Are you getting any specific errors?

[Liyf]

In fact, I choose to use annovar, it is easy for me.Because annovar is written in perl, and I am familiar with it. I suggest you use it, too.

[Madelaine Gogol]

Next time I get some data like that, I'll take a look.

Answer 3

[Swbarnes2]

I use annovar when I do mouse exome sequencing.

http://www.openbioinformatics.org/annovar/

[Liyf]

Thank you. I think sequencing either mouse or human, the workflow is always the same.