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This workflow consists of a series of Snakemake workflows that can be executed using the supplied bash scripts:
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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
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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
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Software used:
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Genome References:
- variant lookup table in VCF format (dbSNP v149, genome build GRCh37.p13)
- hg19 to GRCh38 chain file
- genome sequence (GRCh38.p4 with Decoy sequences)
- splicesites (derived from Gencode version 23 (GRCh38.p3))
- 1000 Genomes Project Phase 3 genotypes:
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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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