Rare Variant Meta-Analysis

ADDED: Optimisations leading to increased performance but increased memory usage

Input Files

-LD matrix : can be obtained from SAIGE step3_LDmat.R

-GWAS summary

Options for RV_meta.R

• --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 SAIGE step3_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'