The commands are in sequence.
| File | Description | Comment |
|---|---|---|
| 0_github.sh | GitHub batch file | |
| 1_make_variant_list.R | Data preparation | |
| 2_lookup.sh | Direct pQTL/Gene lookup | |
| 3a_deCODE.sh | Regional lookup for deCODE | |
| 3b_region.sh | Regional lookup for others | |
| 4_aggregate.sh | Meta-data | |
| 5_coloc.sh | Colocalisation analysis | to be revised |
The pQTL/Gene lookup also accumulates results, so we do
grep '#' 2_lookup.sh | sed 's/#//'upon completion.
This is set by M, and testing results for M=1Mb are contained in the regions/ directory. When M=0, we have another direct pQTL lookup.
Results are in tsv format of named cohorts.