Command-line documentation and usage of GhostKnockoffGWAS
Usage
Simple run
GhostKnockoffGWAS --zfile example_zfile.txt --LD-files EUR --N 506200 --genome-build 38 --out example_outputRequired inputs
| Option name | Argument | Description |
|---|---|---|
--zfile | String | Input file containing Z-scores as well as CHR/POS/REF/ALT. See Acceptable Z-score files for detailed requirement on this file. |
--LD-files | String | Input directory to the pre-processed LD files. Most users downloads this from the Downloads Page |
--N | Int | Sample size for target (original) study |
--genome-build | Int | The human genome build used for SNP positions in zfile (this value must be 19 or 38) |
--out | String | Output file name (without extensions) |
Optional inputs
| Option name | Argument | Description |
|---|---|---|
--CHR | Int | The column in zfile that will be read as chromosome number (note this must be an integer, e.g. chr22, X, chrX, ...etc are NOT acceptable). [If not specified, we will search for a column with header CHR] |
--POS | Int | The column in zfile that will be read as SNP position . [If not specified, we will search for a column with header POS] |
--REF | Int | The column in zfile that will be read as REF (non-effectiv) allele . [If not specified, we will search for a column with header REF] |
--ALT | Int | The column in zfile that will be read as ALT (effective allele). [If not specified, we will search for a column with header REF] |
--Z | Int | The column in zfile that will be read as Z-scores. [If not specified, we will search for a column with header Z] |
--seed | Int | Sets the random seed [If not specified, defaults to 2023] |
--verbose | Bool | Whether to print intermediate messages [If not specified, defaults to true] |
--random-shuffle | Bool | Whether to randomly permute the order of Z-scores and their knockoffs to adjust for potential ordering bias. The main purpose of this option is to take care of potential ordering bias of Lasso solvers. However, in our simulations we never observed such biases, so we turn this off by default.[If not specified, defaults to false] |
--skip-shrinkage-check | Bool | Whether to allow Knockoff analysis to proceed even with large (>0.25) LD shrinkages [If not specified, defaults to false] |
Output format
- A summary file, e.g.
example_output_summary.txt. This file contains broad summary of the analysis - A comma-separated file, e.g.
example_output.txt. This file contains the fullGhostKnockoffGWASoutput, one SNP in each row. - (optional) Manhattan plots, which can be generated by following step 5 of detailed example.
For a more detailed explanation on these 2 files, see Tutorial.