Questions tagged [gwas]
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84
questions
3
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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:
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- 85
3
votes
1
answer
622
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 ...
- 31
1
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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
1
vote
2
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69
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Why does my HWE QQ plot have extreme deviation and what does it mean?
This question was also asked on Reddit
I have recently completed my thesis and one of the comments was that I report on why this graph looks this way. I have tried to find a reason but the closest I ...
1
vote
1
answer
282
views
LD clump GRCh38 GWAS results
The vignette of R package ieugwasr describes a plink based wrapper function for LD clumping GWAS data using the 1000 genomes ...
- 11
2
votes
1
answer
93
views
How are the "effect_allele" and "other_allele" bases chosen in a PGS file from the PGS Catalog?
How are the "effect_allele" and "other_allele" bases chosen in a PGS file from the PGS Catalog?
For example, for PGS002723 (https://www.pgscatalog.org/score/PGS002723/), if I set ...
- 325
2
votes
1
answer
514
views
Getting nearest gene from SNP data using SNP ID, CHR, and BP
I have data from a GWAS that provides me with the SNP, Chromosome, and base-pair. My data set has thousands of SNPs. What is the easiest way to find the nearest gene for each SNP using this ...
- 21
2
votes
2
answers
404
views
How to z-transform Fst and -log(p) values for genome wide selection scan?
I saw in the literature a lot genome wide scans showing $F_{ST}$ values in a 'z-transformed' format which seems to be bounded between 0 to infinity.
Examples are found easily searching for 'genome-...
- 121
2
votes
1
answer
297
views
Genomic inflation factor distribution (lambda)
Considering that the p-value of a chi statistic(df=1) is uniform, the expected genomic inflation factor is λ=1. I show its calculation in R with the next chunk of code:
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- 73
2
votes
0
answers
107
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 ...
0
votes
1
answer
631
views
Identify SNP from genetic position
I am looking for a way to obtain SNP names from their coordinates (Chromosome:BP) - very much the reverse of the question answered here:
(https://stackoverflow.com/questions/20251612/map-snp-ids-to-...
- 103
0
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0
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107
views
Help sought with GWAS and vcf files, lack phenotype labels
This question has also been asked on Biostars
Hi, I am very new to this area, and I am taking a class about bioinformatics. For an independent project assignment, I need to do a GWAS. I am using the ...
2
votes
0
answers
56
views
LD block labels annotation for GWAS summary data
I have a txt file summarising the result of a GWAS on an European population. Its structure is the next one:
...
- 73
0
votes
2
answers
483
views
Lifting snp rsid build 37 to 38
I’m looking to lift over a dataset of GWAS summary stats from build 37 to 38, including converting rsid. Downstream it is to be used for co-localisation with another dataset of build 38.
Would anyone ...
1
vote
1
answer
91
views
Allele effects by parental-origin estimated from genotyping array data
We are dealing with relatively large family data (> 1,000 trios) with genotyping array data.
We would like to see the allele effects on children separately of mothers, fathers, and children, as in ...