Question: User Friendly Tools For Genetic Association Studies
9
gravatar for Thomas
7.5 years ago by
Thomas720
Copenhagen, DK
Thomas720 wrote:

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

genetics association snp gwas • 3.3k views
ADD COMMENTlink modified 5.6 years ago by ben.bob30 • written 7.5 years ago by Thomas720

Thanks for all the nice response. This is indeed a very big help. Thomas

ADD REPLYlink written 7.5 years ago by Thomas720
5
gravatar for Khader Shameer
7.5 years ago by
Manhattan, NY
Khader Shameer18k wrote:

I would happily add tools/databases like

PolyPhen / SIFT : Effect prediction, even though the percentage of coding SNPs are less, will demonstrate this to show some nice tools in the area of effect prediction.

GWAS Catalog : to show the available repertoire of genotype-phenotype data

HuGENavigator : to introduce how the genetic association data is integrated with relevant information

PheGenI : to introduce how GWAS data is integrated with NCBI resources

DistiLD :Very interesting database of diseases and traits in linkage disequilibrium blocks, can be used to discuss various interesting LD regions associated diseases revealed by GWAS.

ADD COMMENTlink written 7.5 years ago by Khader Shameer18k
3
gravatar for Larry_Parnell
7.5 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

We use SAS and HelixTree from GoldenHelix.

Lmekin - a linear mixed model using kinship - is what we use to analyze GWAS data comprised of sets of related individuals. Kinship is often ignored or under-appreciated, but one would do so at one's peril. There are several internet sites with Lmekin info, many in R.

Haploview is preferred for calculation of LD.

We do not like PLINK.

ANNOVAR and VAAST are good for discerning functional consequences of SNP alleles.

Both dbSNP and OMIM have information on the clinical significance of SNPs.

ADD COMMENTlink written 7.5 years ago by Larry_Parnell16k
1

What's wrong with PLINK?

ADD REPLYlink written 7.5 years ago by Caddymob950
1

There is a new R package "GWAF" for performing GWAS. It is based on Lmekinship package. Very user-friendly.

ADD REPLYlink written 7.5 years ago by Kris40

We find it inferior for our datasets, desired outcomes and the models we use to test for association.

ADD REPLYlink written 7.5 years ago by Larry_Parnell16k
3
gravatar for Zev.Kronenberg
7.5 years ago by
United States
Zev.Kronenberg11k wrote:

Second @Larry_Parnell on VAAST. Our lab has a mini course on how to use VAAST to find the causal variant in Miller Syndrome.

SWEEP from Broad is also nice for EHH.

Both of these aren't for classic GWAS.

ADD COMMENTlink written 7.5 years ago by Zev.Kronenberg11k
2
gravatar for Kris
7.5 years ago by
Kris40
Kris40 wrote:

a couple we have used:

Genevar - for discovery and visualization of eQTL data http://www.sanger.ac.uk/resources/software/genevar/

mmimiRNA - a nice tool for inspecting mRNA/microRNA co-expression

ADD COMMENTlink written 7.5 years ago by Kris40

mimirna: http://mimirna.centenary.org.au

ADD REPLYlink written 7.5 years ago by Kris40
0
gravatar for ben.bob
5.6 years ago by
ben.bob30
ben.bob30 wrote:

Also check out variant tools varianttools.sourceforge.net), which provides a complete toolset for association studies.

ADD COMMENTlink written 5.6 years ago by ben.bob30
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