Download PLINK - Psychiatric & Neurodevelopmental Genetics Unit (PNGU)

Appendix B
Order of major operations in PLINK
This section contains a rough flow-chart of some of the main operations in PLINK. In particular, it is designed
to indicate the order in which certain operations are performed (i.e. whether SNPs are excluded before or
after merging files, etc), and also when PLINK halts operation, e.g. after certain commands, meaning that
certain combinations are not feasible.
Most of these steps are optional (i.e. will only occur if a specific command has been issued on the
command line).
• Parse command line, for commands and options
• Check version, unused options, warnings
• Define chromosome set (human, or --mouse, --rice, etc)
• Run ID-helper utility (--id-dict and --id-match), then QUIT
• Run SNP-annotation (--lookup and --lookup-gene), then QUIT
• Run compression/decompressio utility (--compress and --decompress), then QUIT
• Read input, either:
– Dummy dataset(--dummy), or
– Simulated dataset (--simulate), or
– Result files for meta-analysis (--meta-analysis), or
– Result files for gene-based report (--gene-report), or
– Result and annotation files (--annotate), or
– Maps for CNVs (--cfile, --cnv-list), or
– Binary filset (--bfile), or
– PED fileset (--file), or
– LGEN fileset (--lfile), or
– Transposed fileset (--tfile), or
– Maps for generic variants (--gfile), or
– Map and dosage files (--dosage)
• For commands not involving basic SNP or CNV data directly (e.g. --meta-analysis, --annotate,
--dosage, --gene-report, etc) then call the corresponding function directly, then QUIT
279