Entering edit mode
10.2 years ago
Thomas
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760
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
Mostly designed for simple traits, but it is quick and works from VCF files.
https://github.com/jewmanchue/vcflib/wiki