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Diagnostics script for GWAS munging / SNP mapping #56

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pascaltimshel opened this issue Jun 10, 2020 · 1 comment
Open

Diagnostics script for GWAS munging / SNP mapping #56

pascaltimshel opened this issue Jun 10, 2020 · 1 comment
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@pvtodorov
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enhancement New feature or request help wanted Extra attention is needed

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@pascaltimshel
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Write a script to check that munging of GWAS SNPs and mapping to HapMap3 went as expected. Importantly, try to assess 'how much GWAS signal got lost':

  • How many SNPs was lost during mapping?
  • What are the top independent loci in the munged GWAS data?
  • ...
@pascaltimshel pascaltimshel added enhancement New feature or request help wanted Extra attention is needed labels Jun 10, 2020
@pascaltimshel
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pascaltimshel commented Jun 10, 2020 •
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Some relevant tools for LD blocks:

LDstore : http://www.christianbenner.com

LDetect
Approximately independent linkage disequilibrium blocks in human populations
Tomaz Berisa, Joseph K. Pickrell, 2016
https://academic.oup.com/bioinformatics/article/32/2/283/1743626

gwas-snps-loci
A simple tool to compute independent SNP and loci based on GWAS data
https://github.com/perslab/gwas-snps-loci

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@pascaltimshel @pvtodorov