Integrating scRNA-seq with GWAS using LDSC, MAGMA, DEPICT and FUMA

Last update: 05 Feb 2020

Requirements

• LDSC
• MAGMA
• DEPICT
  • PLINK
• Specificity metrices of scRNA-seq data.

The pipeline

All of the code neccesary to reproduce our findings are found within this repository.

LDSC

Follow the steps, including:

• Install LDSC.
• Munge sumstats.
• Estimate heritability and genetic correlations.
• Run the cell type enrichment analyses.

MAGMA

Follow the steps, including:

• Preparing summary statistics.
• A MAGMA sensitivity analysis.
• Running MAGMA in Top 10% and Linear mode.

DEPICT

• Configuration files of all summary statistics and the mapping files used for DEPICT are included in this repository.
• For DEPICT analyses, summary statistics from the MAGMA summary statistics preparation can be used.

FUMA

FUMA was run on their web-based platform.

• Summary statistics from the MAGMA summary statistics preparation can be used as input for the SNP2GENE process.
• The gene analysis result can then be used as input for the Cell type process.