User Friendly Tools For Genetic Association Studies (update)

Question

[Thomas]

Hi all,

I am giving a course presenting various bioinformatic tools applied in genetic association studies. The target audience are phd students with a medical/biological background. Since non of the students have experience within programming/linux/R etc I will like to focus on "user friendly (web-based)" 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
• regulomeDB - Get putative functional annotation for SNPs
• HaploReg - Combine LD (1000G) and regulomeDB

I actually asked the same question 2 years back (User Friendly Tools For Genetic Association Studies) and received some very nice inputs. However, since I am giving the same course again :) I would like to hear if anyone would help renew/expand the existing list.

Thanks a lot
Thomas

[Zev.Kronenberg]

Mostly designed for simple traits, but it is quick and works from VCF files.

https://github.com/jewmanchue/vcflib/wiki