AutoSolar

Description

AutoSolar is automated genome-wide scan (singlepoint and multipoint) software by using SOLAR. AutoSolar.sh uses PedConvert for fast pedigree convert.

Required input files

Pedigree files: chr1.raw, ... , chr22.raw
Map files: map1.dat, ... , map22.dat
Phenotype file
Solar control file

Usage

Command is:

    autosolar.sh [options]

analysis options

--solar-file [file]

Specify solar analysis option (control) file. Default is solar.dat

--ibd

Calculates IBDs and MIBDs before scan

--ibd-dir [full path to IBD directory]

Specify IBD directory where pre-calculated Solar IBD files are located. Example --ibd-dir /home/james/ibd/



--mibd-dir [full path to MIBD directory]
Specify MIBD directory where pre-calculated Solar MIBD files are located. Example --mibd-dir /home/james/mibd/


--polygenic-only
Polygenic screening only, no IBD/MIBD or linkage scan done.

--interval [cM]
Specify multipoint mapping interval in cM (Default is 5)

--finemap [lod]
Specify lod score treshold for finemapping (This is disabled by default, but specifying finemap lod will enable it)

--chr [start] [stop]
Specify range of chromosomes to be analysed. Chromosome X is 23 and default range is 1 22

--analysis [single,multi]
Specify single or multipoint analysis only, default is both.

--only [males,females]
If males are used, phenotypes of females are set to unknown and if females is used, phenotypes of males are set to unknown.

--pedcheck-cmd [name]
Specify pedcheck command.

--skip-pedcheck
Skip Mendelian check (usefull if genotype data is known to be consistent and pedigrees are big!)

--pedcheck-level [level]
Specify PedCheck check level.

--solar-cmd [name]
Specify solar command (Default is solar)

Input/Output file control options

--phen [file] 
Specify different phenotype file name than default phen.dat.

--ignore
Pedigree file includes qualitative or quantitative as a first phenotype before marker genotypes. It will be read and ignored. Phenotype are always read from phenotype file.

--ext [extension]
Pedigree file extension, example: raw or pre. Default is raw.

--makefilesonly
Make input files only. Does not run analysis. Usefull to test you data before analysis.