All Questions
8
questions
3
votes
1
answer
120
views
How to perform liftover from 38 to 37 in R?
I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code:
...
- 85
2
votes
1
answer
630
views
GWAS in python?
A question similar to this has also been asked on Biostars
I understand GWAS is done with R, but are any written in Python?
I'm used to python and java, acclimating to R will take a bit of time and my ...
- 29
0
votes
1
answer
326
views
Polygenic Risk Scores
I have run a GWAS and used PRSice (https://www.prsice.info/) to calculate polygenic risk scores on the data collected from the GWAS. I need to check whether alcohol dependence can predict gambling ...
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
1
answer
127
views
GWAS MAC filter Interpretation
I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~...
- 147
1
vote
1
answer
2k
views
Convert VCF to genotype table
How can I convert a VCF file into a genotype table (SNP matrix)?
I have this format:
...
- 147
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