All Questions
14
questions
1
vote
0
answers
43
views
PLINK linear association testing command with an interaction and 2 covariates term
I am trying to write the right command for my association testing using PLINK 1.9 but I could not find a clear answer so far and not sure how to wrtie it correct.
I have genotype variants called and ...
- 23
2
votes
0
answers
111
views
Input for --score in PLINK 1.9 when generationg PRS using GWAS summary statistics
I'm conducting a simulation and I need to obtain polygenic risk scores (PRS) using genome wide association studies (GWAS) summary statistics.
It is known that the GWAS will give BETA and OR for ...
1
vote
1
answer
797
views
Plink error: --check-sex/--impute-sex requires at least one polymorphic X chromosome locus
I am running an analysis in plink.
This is my first attempt at a QC and I keep encountering the same message when I try to go through with my sex check. I've done the SNP missingness step, it's this ...
- 67
0
votes
1
answer
59
views
Publicly available genotype / phenotype dataset?
I'm looking for publicly available genotype data (eg. 1000 Genomes or HapMap) that also has associated phenotypes (any traits). I'm wanting to use it as a test run for a GWAS pipeline. Does anyone ...
1
vote
1
answer
1k
views
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
1
answer
79
views
Random GWAS data generator
I was wondering if there is a tool/script/program that randomly generates GWAS data. The purpose of such a tool would be to use it for educational purposes. So you generate some random .ped, .map and ...
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
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
1
vote
0
answers
34
views
GWAS Rooted PCA analysis problem
I'm fairly new to plink software and wanted to get some additional practice after doing several tutorials. I obtained the data from this paper (I'm not using this paper's methods) to do some QC with ...
- 11
1
vote
1
answer
70
views
Question: How to simulate 100k samples having 40 million SNPs in a proportion of case:control=30:70?
Note: this question can also be found on Biostars
I need to perform a stress test in a GWAS tool and the duty demands a dataset (plink format) having 100 thousand samples, having 40 million SNPs in a ...
- 207
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
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
2
answers
2k
views
PLINK clump behavior on missing SNPs?
I have a long list of autoimmune-associated SNPs, and I want to boil it down so that I get one SNP representing each LD block. I chose to use PLINK's --clump option for this. I'm roughly following ...
- 380
5
votes
3
answers
2k
views
Is there any difference between SNPs 'AG' and 'GA' in association analyses?
I am using plink to check the association between a phenotype and the SNPs of a gene. plink says the phenotype is significantly associated with a SNP on that gene, and when I check the SNP alleles, ...
- 305