TABLE 2.

Comparison between genetic software for various usages.

	Genetic software
Usage	bgenix	QCTOOL	PLINK
Extract SNPs	Yes, very quickly, although can only specify up to 9,980 SNPs by chromosome and position identifier	Yes, and has useful wildcard feature to extract from all chromosome files in one step, but slow	Yes, have to extract per chromosome, slow for BGEN data as it has to auto-convert the entire file not just the required SNPs
Conduct QC	No	Yes, it computes summary statistics but filtering has to be done in a separate step, and with additional tools (such as awk or R)	Yes, fast, it can compute summary statistics and apply filtering. Not all commands are suitable for use on imputed data
Compute PRS	No	Yes but poorly documented	Yes, with many options