Beginner for SnpEff

Question

[basalganglia]

Hi everyone,

At first, I want to say I am so beginner for using linux and setting up tools :)

For doing variation I will use snpEff tool with another server, however I have certain problems and I have been complicated

1. I don't understand how can I configure snpEff.config file
2. I have vcf file, but I don't understand where I will put in which file, it can be in snpEff file?
3. I have to download reference genome hg19, is that right? But I don't know where I will put it in which folder :( (Also I have problem with downloading reference genome ,so ı have to it manually and I have Homo_sapiens.GRCh37.71.gtf.gz reference file.

So I have basic problems for installation of this tool.

Many thanks

[Ram]

If you're a beginner to Linux, I'd strongly recommend getting help from a Linux pro near you and learning from them. We can help you out, but you're going to need a deep understanding than what can be explained over a discussion forum and a Linux dabbler next to you will help you get a perspective on the quirks and nuances of the beautiful world of Linux!

Oh, and of course, welcome to Linux!

Answer 1

[iraun]

I suppose you have already read this snpEff documentation. Just copy paste the commands of the web and you will have snpEff installed:

# Download latest version
wget http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip

# Unzip file
unzip snpEff_latest_core.zip

Once you have installed, you need to download the database of interest, in your case GRCh37.71. To do this use the next command:

java -jar snpEff.jar download GRCh37.7

Now that you have the database downloaded, you can run snpEff using your vcf file as input.If you run SnpEff from a different directory than your install directory, you have to specify where the config file is located using the -c command line option:

java -Xmx4g path/to/snpEff/snpEff.jar -c path/to/snpEff/snpEff.config GRCh37.7 path/to/YOURFILE.vcf > OUTPUT.EFF.vcf

I've show you the general steps, but I strongly recommend you to take a look to snpEff documentation, since it is very well and clear explained for beginners.