Questions tagged [ld]
The ld tag has no usage guidance.
4
questions
2
votes
0
answers
47
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
4
votes
1
answer
178
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Using QCTOOL v2 to process UK Biobank .bgen files - why so slow?
I’m currently using QCTOOL v2 to process imputed .bgen files from UK Biobank, however they seem to be processing very slowly. Is this normal?
My command is pretty basic; I’m filtering out a list of ...
- 61
3
votes
1
answer
34
views
SNPs in LD in which populations?
I have 3 SNPs that are in LD in 'several' populations here:
https://www.ebi.ac.uk/gwas/variants/rs13078854#ld_panel_label
It's a pain to look at all (30) populations one by one to manually check if ...
- 440
2
votes
0
answers
95
views
how to plot LD between SNPs and CNVs
I have a bunch of CNVs which I have estimated LD between each allele of CNV with all SNPs across the entire human genome. I used my R-script to do a pairwise LD analysis.
The following is the first ...
- 496