Questions tagged [ld]

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LD local clump-GRCh38 bfile

I want to do LD local clumping. The tutorial (https://mrcieu.github.io/ieugwasr/articles/local_ld.html) teaches how to, but the downloaded bfile is GRch37. I followed this question to download GRch38. ...
Phylicia_SY's user avatar
1 vote
1 answer
217 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 ...
Joonatan's user avatar
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: ...
Gero's user avatar
  • 73
4 votes
1 answer
515 views

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 ...
Cat's user avatar
  • 61
3 votes
1 answer
40 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 ...
Dan Bolser's user avatar
2 votes
0 answers
118 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 ...
Anna1364's user avatar
  • 516