Step 4: spatial_ldsc

usage: gsmap run_spatial_ldsc [-h] --workdir WORKDIR --sample_name SAMPLE_NAME
                              --sumstats_file SUMSTATS_FILE --w_file W_FILE
                              --trait_name TRAIT_NAME [--n_blocks N_BLOCKS]
                              [--chisq_max CHISQ_MAX]
                              [--num_processes NUM_PROCESSES]
                              [--use_additional_baseline_annotation [USE_ADDITIONAL_BASELINE_ANNOTATION]]

Named Arguments

--workdir

Path to the working directory.

--sample_name

Name of the sample.

--sumstats_file

Path to GWAS summary statistics file.

--w_file

Path to regression weight file.

--trait_name

Name of the trait being analyzed.

--n_blocks

Number of blocks for jackknife resampling.

Default: 200

--chisq_max

Maximum chi-square value for filtering SNPs.

--num_processes

Number of processes for parallel computing.

Default: 4

--use_additional_baseline_annotation

Use additional baseline annotations when provided

Default: True