GAINQC - Quick Reference

There are 3 groups of command line options for GAINQC, viz., required file, optional files and output control. The following is a summary of all available GAINQC command line switches and their meanings, sorted by groups.

Required Files

-geno genotypeFile

Selects the input genotype file in the matrix format.

-snps snpFile

Selects the input snp information file.

-ped pedFile

Selects the input pedigree file.

Optional Files

--settings settingsFile

Selects the settings file which contains user altered thresholds in the KEY=VALUE format.

--quality qualityFile

Selects the genotype quality scores file.

--hapmap externalGenotypesFile

Selects the external genotypes file in the hapmap genotype data format for comparing gentoype calls.

--ignoreSamples ignoreFile

Select the file containing sample Ids to be ignored.

Output Control

--prefix outputPrefix

Sets the prefix for all the output files to be outputPrefix.

--skipRelatednessCheck

Tells the program not to perform any relationship checks.

--TDT

Tells the program to compute all TDT statistics and perform related tests.

--association

Tells the program to perform association tests using labels in the pedigree file.

--output

Tells the program to output filtered genotype and quality score (if available) files.

--logSize fileSize

Specifies the maximum size of detailed log file (in MBs).