What’s the answer? (user friendly genetics tools)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question:

“user friendly” tools for genetic association studies

Dear all

I am giving a course about bioinformatic tools used for genetic association studies. The target audience are phd students with a medical/biological background. Since non of these have experience within programming/linux/R etc I will like to stick to “user friendly” tools like the following:

SNAP – investigate LD, find out whether a SNP is on GWAS arrays
Hapmap, haploview – select tag SNPs
locusZOOM – visualize association plots
UCSC – investigate the properties/positions etc of SNPs
plink – make association studies and QC for GWAS data
NHLBI Exome Sequencing Project (ESP) – Get sequence derived SNP information

I know the list could probably be expanded with 100s of good ideas and the term “user friendly” is very subjected, I know.

But, please fill in. I would very much like to hear from you

All the best
Thomas

There was a nice set of answers that covered a range of issues in this arena. Check out the answers. And it is a question that a number of people have “favorited” at BioStar so they thought it had valuable information. As with all bioinformatics tools, not all of them will be relevant to your work–but there might be some that could be very useful. I also liked that the intent of the question was to unearth tools that don’t require programming skills, which many users just don’t have.