Questions tagged [ld]

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2 votes
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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

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

SNPs in LD in which populations?

I have 3 SNPs that are in LD in 'several' populations here: It's a pain to look at all (30) populations one by one to manually check if ...
2 votes
0 answers

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