Questions tagged [gwas]
The gwas tag has no usage guidance.
7
questions
5
votes
2
answers
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What does PCA mean on GWAS
I understand what GWAS is and I'm able to perform certain tests with the p-values, etc. But what I am having a hard time wrapping my head around is what PCA on GWAS means.
So let's say I have 100,000 ...
- 341
5
votes
1
answer
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Adjusting phenotypes by regressing out covariates
I'm trying to use the bfGWAS tool, which analyses GWAS data and integrates functional annotations to identify casual SNPs (paper and
github). In the user manual, it states:
We recommend first ...
- 153
5
votes
3
answers
216
views
Where can I find a database that has phenotype information together with associated SNPs?
I have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association....
- 521
1
vote
2
answers
255
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Simulating phenotype with the 1000 Genomes Project
I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation?
I'm trying to use ...
- 207
1
vote
1
answer
1k
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Making PLINK compatible files from VCF file without phenotype information
I have a big VCF file that I need to convert to, preferably, bed/bim/fam files that are readable by plink. Currently using plink 2. I am aware that this version of plink can be used to convert VCFs ...
- 11
1
vote
2
answers
263
views
Interpreting GWAS results with different settings
I did a bunch of GWAS analysis (linear model without covariates) with applying different quality controls. How to choose the optimal settings when filtering for minor allele frequency (maf), Hardy-...
- 147
0
votes
0
answers
222
views
GWAS phenotype data format and preprocessing
I have a set of different phenotypes which I want to use for a GWAS analysis (general linear model). I have a couple of questions and uncertainty about the phenotype data input.
I have control and ...
- 147