Step 6: gsMap report (optional)

usage: gsmap run_report [-h] --workdir WORKDIR --sample_name SAMPLE_NAME
                        --trait_name TRAIT_NAME --annotation ANNOTATION
                        [--top_corr_genes TOP_CORR_GENES]
                        [--selected_genes [SELECTED_GENES ...]]
                        --sumstats_file SUMSTATS_FILE [--fig_width FIG_WIDTH]
                        [--fig_height FIG_HEIGHT] [--point_size POINT_SIZE]
                        [--fig_style {dark,light}]

Named Arguments

--workdir

Path to the working directory.

--sample_name

Name of the sample.

--trait_name

Name of the trait to generate the report for.

--annotation

Annotation layer name.

--top_corr_genes

Number of top correlated genes to display.

Default: 50

--selected_genes

List of specific genes to include in the report (optional).

--sumstats_file

Path to GWAS summary statistics file.

--fig_width

Width of the generated figures in pixels.

--fig_height

Height of the generated figures in pixels.

--point_size

Point size for the figures.

--fig_style

Possible choices: dark, light

Style of the generated figures.

Default: 'light'