Munging full summary stats is way too slow

[PhoebeGuo97]

I'm try to munge my full summary stats by fullSS_path <- MungeSumstats::format_sumstats(path = fullSS_path, ref_genome = "GRCH37"). I left my MacBook on overnight and it's still running.

The following is what I see in R Console: First line of summary statistics file: uniqID.a1a2 CHR BP A1 A2 SNP Z P Nsum Neff dir EAF BETA SE
Summary statistics report:

• 13,367,299 rows
• 13,354,030 unique variants
• 2,394 genome-wide significant variants (P<5e-8)
• 22 chromosomes Checking for multi-GWAS. Checking for multiple RSIDs on one row. Checking SNP RSIDs. 11,599 SNP IDs are not correctly formatted. These will be corrected from the reference genome. 165,861 SNP IDs appear to be made up of chr:bp, these will be replaced by their SNP ID from the reference genome Checking for merged allele column. Checking A1 is uppercase Checking A2 is uppercase Ensuring all SNPs are on the reference genome. Loading reference genome data.

[bschilder]

How long you expect this to take depends on your computer specs (part of the reason for the Issues template). Also, if you find an issue with MungeSumstats, you should submit it to the MungeSumstats repo: https://github.com/neurogenomics/MungeSumstats