coloc.susie.direct

Colocalization on Susie results from FinnGen fine-mapping pipeline. This repository hosted the code only.

Inputs

json

• colocInfo1: coloc information for paired trait1, format: dataset name, dataset type, resource link
• colocInfo2: coloc information for paired trait2
• nColocPerBatch: number of coloc pairs distached to each VM node, default 1000
• excludeSameNameTrait: exclude the traits with the same name, default true
• h4pp_thresh: H4 PP threshold to merge the coloc results, default 0.5
• cs_log10bf_thresh1: log10bf threshold for credible set in finemapped cs1:cs1 pair, default 0.9
• cs_log10bf_thresh2: log10bf threshold for other pair, default 1.0
• docker: ** refinery: europe-docker.pkg.dev/finngen-refinery-dev/eu.gcr.io/coloc.susie.direct:0.1.8 ** sandbox: eu.gcr.io/finngen-sandbox-v3-containers/coloc.susie.direct:0.1.8

Outputs

• pairs: Array of File, region matched for each dataset
• N: Array of Int, indicate number of pairs in region
• coloc: Array of File, coloc results for each pair
• hit: Array of File, coloc top signals in each pair
• colocQC: File, QC and merged coloc results from all dataset

Submit to SandBox

# download the code
# be in the folder: cd coloc.susie.direct
# move the wdl to the script folder
mv wdl script
cd script
./submit META.json Trait Type gs://YOUR_BUCKET_can_write/demo/test_project

Contacts

zhili[dot]zheng[at]broadinstitute[dot]org