AutoMerlin

Description

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.

Required input files

Usage

Command is:

    automerlin.sh [options]

Quantitative trait specific options

--vc

Variance component (VC) linkage analysis

--cov

Use covariates, first phenotype in phenotype file is selected as trait and rest of the phenotypes are covariates, otherwise all phenotypes are analyzed separately.

--sex

Add sex as covariate

Qualitative (discrete) trait specific options

--npl (same as --discrete)

Non-parametric ('model-free') linkage analysis

--model [file]

Parametric ('model-based') linkage analysis

Other analysis options

--chr [start] [stop]

Specify range of chromosomes to be analysed. Chromosome X is 23 and default range is 1 22

--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.

--analysis [single,multi]

Specify single or multipoint analysis only, default is both.

--trim

Toggle on MERLIN --trim option

--information

Toggle on MERLIN --information option

--pedstats

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.

--error

Genotyping error analysis

--wiped

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.

--bits [number]

Set bits for analysis.

--missing [variable]

Specify missing value.

--simulate

Genome-wide scan simulation using Merlin --simulate option.

--replicates [number]

Specify number of replicates for simulation.

--merlin-extra [file]

Extra analysis option file for Merlin. All extra commands have to be in first line of the file.

--merlin-over [file]

This will override all Merlin analysis options, all merlin commands have to be first line of the file.

--disable-map-position [number (cM)]

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

--merlin-cmd [name]

Specify merlin command. Usefull if one have default merlin binary as merlin and 64-bit version is named as merlin64

--xmerlin-cmd [name]

Specify X-chromosome merlin command.

--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.

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.

--pdf

Toggle on MERLIN --pdf option