Additinal Input files

PAR file

This is S.A.G.E. parameter file which is an optional file to run a segregation analysis in ONETOOL. It is a text file containing a list of S.A.G.E. SEGREG instructions written according to a specific syntax (i.e., instruction blocks).

For the detailed description of the PAR file, see the S.A.G.E. user manual.

Note

When a par file is not specified, ONETOOL runs the default analysis in SEGREG which is the comingling analysis.

$ onetool --fam test_miss00.fam --pheno test_miss00.pheno --pname t2d --segreg --par segreg.par

TYP file

This is S.A.G.E. trait genotype probability file which is required to run a model-based linkage analysis in ONETOOL. It is a text file containing the individual specific type probabilities conditional on the model and all pedigree information available, and individual specific penetrance information. This file is prodiced by a segregation analysis.

For the detailed description of the PAR file, see the S.A.G.E. user manual.

$ onetool --fam test_miss00.fam --vcf test_miss00.vcf -lodlink --typ test_segreg.typ

MERLIN MAP file

This is MERLIN genetic map file which is required to run a model-free linkage analysis in ONETOOL.

For the detailed description of this MAP file, go to MERLIN.

Note

The PLINK MAP file contains 4 columns while the MERLIN MAP file contains 3 columns (sex-average) or 5 columns (sex-specific). The PLINK MAP file with the correct genetic map information in 3rd column can be used for the model-free linkage analysis in ONETOOL.

$ onetool --fam test_miss00.fam --vcf test_miss00.vcf --merlin --map test_miss00.map

SET file

This is a required file to run gene-based association analyses for rare variants. It contains the SNP clustering information in genes in the following format:

1. Gene ID
2. SNP ID

$ onetool --fam test_miss00.fam --vcf test_miss00.vcf --genetest --set test_gene.txt