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Shiny/GENEX-FB2
Snakefiles
.gitattributes
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GTcheck.sh
Genotyping.sh
README.md
SMR.sh
cluster_config.yaml
config.yaml
eQTL.sh

README.md

Workflow for eQTL analyses in the developing human brain

  • This workflow consists of a series of Snakemake workflows that can be executed using the supplied bash scripts:

  • Genotyping.sh: run initial genotyping QC and prepare data for imputation

  • eQTL.sh: QC and filtering of post-imputation genotypes and expression data; eQTL analysis

  • GTcheck.sh: map reads to reference, call snps, and compare to imputed genotypes

    • This needs to be run after eQTL analysis because it requires processed vcf files from eQTL workflow
  • SMR.sh: SMR analyses of eQTL data (requires config file that will be made available on publication)

  • Expression data were created from the workflows detailed here

  • Software used:

  • Genome References:

  • GTEx data:

    • SNP lookup table (GTEx_Analysis_2016-01-15_v7_WholeGenomeSeq_635Ind_PASS_AB02_GQ20_HETX_MISS15_PLINKQC.lookup_table.txt.gz)
    • significant eQTLs (GTEx_Analysis_v7_eQTL.tar.gz)
    • Metasoft multi-tissue eQTL data (GTEx_Analysis_v7.metasoft.txt.gz)
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