SNPMStat_CC

Input

The input files plink.recode.tped and plink.recode.tfam are mandatory. The genotypes in plink.recode.tped can be either A, C, G, T or 1, 2, 3, 4 and the phenotype in plink.recode.tfam should be coded by PLINK default, namely 1=unaffected, 2=affected. -s indicates that the file strand.txt which lists the strand orientation relative to the reference panel is available. This file contains a line for each SNP, in the same order as in plink.recode.tped, with only one entry, 0 = consistent with reference panel, 1 = inconsistent. By default, SNPMStat_CC assumes consistency for all SNPs (fills all strand_orientation entries with 0).

Output

SNPMStat_CC outputs to case_control.dat.

Options

Option	Default	Description	Example
-s	uniform consistency	Indicate that the file strand.txt listing strand orientation is available.	SNPMStat_CC -s

Example

The example input and output data files can be found in the zipped package below and can be run by the command

Note that this output file has been renamed to case_control_CC.dat in the package below because it is different from the example case_control.dat file for SNPMStat.

Download

SNPMStat_CC for Windows [updated 09 July 2008]

SNPMStat_CC for Linux [updated 09 July 2008]

Example files [updated 09 July 2008]