8000 Diagnostics script for GWAS munging / SNP mapping · Issue #56 · perslab/CELLECT · GitHub
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Diagnostics script for GWAS munging / SNP mapping #56

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Diagnostics script for GWAS munging / SNP mapping#56
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pvtodorov
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enhancementNew feature or requesthelp wantedExtra attention is needed

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@pascaltimshel
pascaltimshel
opened on Jun 10, 2020

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?
  • ...

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  1. pascaltimshel
    added
    enhancementNew feature or request
    help wantedExtra attention is needed
    on Jun 10, 2020
  2. pascaltimshel
    assigned
    pvtodorov
    on Jun 10, 2020

  3. pascaltimshel commented on Jun 10, 2020

    @pascaltimshel
    pascaltimshel
    on Jun 10, 2020
    CollaboratorAuthor

    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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