ADDED: Optimisations leading to increased performance but increased memory usage
-LD matrix
: can be obtained from SAIGE step3_LDmat.R
-GWAS summary
--anno_file
: Annotation file (same format SAIGE accepts https://saigegit.github.io/SAIGE-doc/docs/UK_Biobank_WES_analysis.html)--annos
: Annotation string to subset variant's by--chr
: chrmosome number--num_cohorts
: number of cohorts--chr
: chrmosome number--info_file_path
: path to the marker_info.txt file generated from SAIGE 'step3_LDmat.R'. Need to specify marker_info.txt file from each and every cohort delimited by white-space (' '
)--gene_file_prefix
: prefix to the LD matrix separated by genes (also generated from SAIGEstep3_LDmat.R
) usually same as marker_info.txt file's prefix--gwas_path
: path to the GWAS summary. Need to specify GWAS summary file from each and every cohort delimited by white-space (' '
)output_prefix
: directory for output
example command could be found in 'test_run.sh'