PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores

BMC Bioinformatics

Table 1 PRSoS optional data output

PRS_0.001	PRS_0.001_flag	PRS_0.5	PRS_0.5_flag	Discard
rs1115507	A1	rs1115507	A1	rs2503243
rs17692694	A2	rs11661323	A2	rs519113
rs4544201	A2	rs12296077	A1
rs6683133	A1	rs12611811	A1
rs7609940	A2	rs17024456	A1
rs7620685	A1	rs17692694	A2
		rs4544201	A2
		rs6683133	A1
		rs7609940	A2
		rs7620685	A1

Example of the SNP log included in the PRSoS output. The SNP log records the SNPs that are used in the PRS at each p-value threshold and whether the first allele column (“A1”) or the second allele column (“A2”) in the target data was scored. SNPs are recorded in the Discard column if the SNPs are discarded due to non-matching alleles between the discovery and the target data

ISSN: 1471-2105