BMD GWAS from Morris et al. summary stats
Adapted from the tutorial using GTEx v8 MASH models
1.) subset_gwas.R
Subsets a full summary stats file to only the needed column for SPrediXcan including effect allele, non-effect allele, chromosome, position, standard error, and effect size. It will output a tab delimited file, which is required for SPrediXcan.
2.) harmonization.sh
Formats the GWAS summary statistics for the MetaXcan pipeline including creating a panel_variant_id.
3.) imputation.sh
Imputes summary statistics. "Summary statistics imputation works in a "region-wide" approach, each region a conceptual computation unit. Imputation takes all variants from the GTEx reference in a chromosomal region (we use Berisa-Pickrell LD blocks) and impute missing GWAS variants using present GWAS variants and genotypes from GTEx. Our implementation allows to split the imputation of a full GWAS in "sub-batches", i.e. just imputing for a few regions. By splitting the execution in smaller units, we can parallelize in an HPC environment."
4.) imp_post.sh
The imputation script splits jobs into smaller units. This script gathers them together and processes them.
5.) SPrediXcan.sh
Runs SPrediXcan on each of the 49 tissues in GTEx v8 using a loop. 49 tissues are listed in tissue_list.txt
6.) MultiXcan.sh
Runs MultiXcan using SPrediXcan outputs from each of the 49 tissues. MultiXcan leverages multiple tissues simultaneously, exploiting cross-tissue QTL sharing.