Questions tagged [gwas]
The gwas tag has no usage guidance.
84
questions
3
votes
1
answer
112
views
What is the state of the art for GWAS in terms of the statistical algorithm for either Case/control and Quantitative traits?
This question was also asked on Biostars
I'm trying to understand what is the best algorithm for GWAS nowadays.
I know we have many tools available like Plink and Hail, but currently, what is the ...
- 207
0
votes
2
answers
92
views
CRISPR screening and systems biology
I am not sure how to tackle this one, so I’ll explain the general idea I have in mind.
Given results of a CRISPR knockout screening experiment (like in this paper) with two types of assays: control ...
- 1,447
1
vote
2
answers
255
views
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
0
votes
1
answer
65
views
significant SNPs to annotated candidate genes
I have performed GWAS and got some significant SNPs. How can I get candidates genes in the flanking regions of those SNPs and also their functional annotations (eg. KEGG).
1
vote
1
answer
145
views
Pandas automatically rounds GWAS P-value
I am working with a specific GWAS. If I were to run this on the command line
grep <rs_id_of_interest> GWAS.txt
I would see the GWAS p-value to be on the ...
- 113
5
votes
2
answers
3k
views
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
2
votes
1
answer
328
views
PLINK - Transposed BED file?
I'm currently working with the PLINK file system to store large amounts of genotype data.
The plain format consists of three files, two files for storing phenotype and marker information as well as ...
- 123
2
votes
1
answer
673
views
how do I convert a vcf file for a GWAS study (using R package vcfR)
I have a vcf file with individual level genetic data, that I read using the R package vcfR
...
- 121
3
votes
1
answer
3k
views
What does liability mean in GWAS heritability?
I am reading about GWAS in heritability. They usually say to calculate heritability on a liability scale but after searching for this word "liability", I still don't understand clearly what does ...
- 55
2
votes
1
answer
247
views
Parallel in PLINK for linear association for SNP effects
I am doing linear association calculations for SNP effects, I see it take a lot of time to do, does anyone have any experience in parallelizing this job. I have used ...
- 55
6
votes
0
answers
107
views
making my own population allele frequency table for input to IADMIX from Gnomad data (population admixture)? [closed]
Hi I'm a first time user of IADMIX. I tested on one known Finnish sample from the 1000Genome project using the softwares provided frequency table hapmap3.8populations.hg19.freqs and the prediction is ...
- 61
1
vote
1
answer
303
views
Odds ratio calculations in GWAS paper
Posting here because the reddit thread I made didn't gain any traction.
I'm having a little bit of trouble understanding how the odds ratio was calculated in this table, specifically the OR marked ...
3
votes
3
answers
1k
views
Is there a way to do GWAS on phenotype data that is not normally distributed?
Is there a way to do GWAS on phenotype data that is not normally distributed?
For example, if you were measuring a trait as a proportion, and the majority of the data consisted of 0.00 with a long ...
- 69
3
votes
1
answer
198
views
Estimating computing resources needed for a GWAS?
One of my dissertation papers is going to involve a GWAS. I have never actually run a GWAS before, and do not know how to estimate the computing resources I need for it. I asked someone on my ...
- 195
3
votes
2
answers
2k
views
How to filter info score post-imputation?
this is a very basic question, but I cannot find it explicitly stated anywhere: When exactly should I filter the info scores after imputation?
I did imputation in Impute2 and am planning on using ...
- 31