All Questions
6
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
0
votes
1
answer
645
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
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
3
votes
1
answer
647
views
How to estimate the phenotypic variation explained by top SNPs from a GWAS study?
I have conducted a large-scale GWAS study and got a few significantly associated SNPs. I used GEMMA with -lmm 1 options to run ...
- 75
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
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