AutoMerlin is automated genome-wide scan (singlepoint and multipoint) software by using MERLIN using non-parametric (NPL), parametric or variance component (VC) linkage analysis. AutoMerlin.sh uses PedConvert for fast pedigree convert.
Command is:
automerlin.sh [options]
Variance component (VC) linkage analysis
Use covariates, first phenotype in phenotype file is selected as trait and rest of the phenotypes are covariates, otherwise all phenotypes are analyzed separately.
Add sex as covariate
Non-parametric ('model-free') linkage analysis
Parametric ('model-based') linkage analysis
Specify range of chromosomes to be analysed. Chromosome X is 23 and default range is 1 22
If males are used, phenotypes of females are set to unknown and if females is used, phenotypes of males are set to unknown.
Specify single or multipoint analysis only, default is both.
Toggle on MERLIN --trim option
Toggle on MERLIN --information option
Pedigree statistics analysis with PedStats. This is very usefull option to check your pedigree, genotype and phenotype statistics and Hardy-Weinberg test statistics for each marker.
Genotyping error analysis
Performs linkage analysis based on error analysis. Error analysis must be done first, then pedwipe is used to eliminate genotypes from pedigree file analysis is performed.
Set bits for analysis.
Specify missing value.
Genome-wide scan simulation using Merlin --simulate
option.
Specify number of replicates for simulation.
Extra analysis option file for Merlin. All extra commands have to be in first line of the file.
This will override all Merlin analysis options, all merlin commands have to be first line of the file.
Disable specific marker from analysis with some map position. This will write S2 to MERLIN locus file on that marker. Map position is read as a string and not as a floating point number, so -99.00 is different than -99
Specify merlin command. Usefull if one have default merlin binary as merlin
and 64-bit version is named as merlin64
Specify X-chromosome merlin command.
Specify pedcheck command.
Skip Mendelian check (usefull if genotype data is known to be consistent and pedigrees are big!)
Specify PedCheck check level.
Specify different phenotype file name than default phen.dat.
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.
Pedigree file extension, example: raw or pre. Default is raw.
Make input files only. Does not run analysis. Usefull to test you data before analysis.
Toggle on MERLIN --pdf option