AutoMerlin.sh is automated QTL genome-wide scan (singlepoint and multipoint) software by using MERLIN. AutoMerlin.sh uses PedConvert for fast pedigree convert.
Command is:
automerlin.sh [options]
% automerlin.sh -h
################################################################################
# Program : AutoMerlin.sh - Automated genome-wide QTL scan with Merlin #
# Version : 1.0 #
# Date : 5.7.2004 #
# Author : Tero Hiekkalinna #
# Email : Tero Hiekkalinna@Helsinki.FI (tero hiekkalinna@ktl.fi) #
# #
# COPYRIGHT (c) Tero Hiekkalinna 2003-2004 #
################################################################################
################################################################################
# Default merlin options are:
# -x x --vc --markerNames --quiet --swap --information --bits 40
# Default pedstats options are:
# --hardyWeinberg --checkAll --showAll
# Results folder: /home/tjuu/omat/automerlin/test2/all_results
################################################################################
Usage: automerlin.sh [options]
Options:
--cov Use covariates, first phenotype in phen.dat is selected
as TRAIT and rest of the phenotypes are covariates,
otherwise all phenotypes are analyzed separately
--sex Add SEX as covariate
--only [males,females] If males are used, phenotypes of females are set to
unknown and vice versa
--makefilesonly Make only Merlin input files
--dicotomous Pedigree file includes dicotomous trait as a first
phenotype. It will be read and ignored
--ext [extension] Pedigree file extension, example: raw or pre. Default
is raw
--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 default Merlin analysis options,
ALL merlin commands have to be first line of the file
--chr [start] [stop] Specify range of chromosomes to be analysed. Example
analyze chromosomes between 5-12: --chr 5 12
Chromosome X is 23. Default is --chr 1 22
--phen [file] Specify your own phenotype file name. Default is
phen.dat
--analysis [single,multi] Specify single or multipoint analysis only, default
is both.
--pedstats Pedigree statistics analysis (PedStats)
--error Genotyping error analysis
--wiped Performs scan based on --error analysis. Error analysis
must be done first
--bits [number] Set bits for Merlin analysis. Current value is 40
--missing [variable] Specify missing value. Current value is x
--simulate Genome-wide scan simulation
--replicates [number] Specify number of replicates for simulation. Default
value is 1
--help or -h This help
Example of genome-wide scan, ALL chromosomes, sex added as covariate:
automerlin.sh --sex
%
If no command line option are specified, genome-wide scan is performed with default merlin options (see Merlin dicumentation). See above.
Enables use of covariates in QTL analysis. First phenotype in phenotype file is selected as TRAIT and rest of the phenotypes are covariates. If covariate option is not used and phenotype file has more than one phenotype, all phenotypes are analyzed separately.
Enable sex as covariate.
If males are used, phenotypes of females are set to unknown and if females is used, phenotypes of males are set to unknown.
Makes only Merlin input files, no analysis performed.
If pedigree file includes dicotomous trait column (no liability class!) before marker loci columns, it will be read and ignored.
Default pedigree file extension is raw, but if pedigree files are named as chr1.pre, chr2, etc., use this option to override it, example: --ext pre
If you want to specify extra Merlin options to default options, create file where you list all extra options in first line of the file, example:
==============================BEGIN OF THE FILE================================= --grid 1 ============================== END OF THE FILE=================================
And command line would be: --merlin-extra merlin.extra.file
If you want to specify ALL Merlin options to replace default options, create file where you list all options in first line of the file, example:
==============================BEGIN OF THE FILE================================= -x x --vc --bits 20 --markerNames --quiet ============================== END OF THE FILE=================================
And command line would be: --merlin-over merlin.over.file
If you want to analyze only chromosomes between 2 and 16, use this option like: --chr 2 16. Or if one only wants to analyze chromosome 21: --chr 21 21. Chromosome X is number 23. Default is --chr 1 22.
If one wan to specify different phenotype file name than default phen.dat. Example: --phen phen_fin.txt.
Specify single or multipoint analysis only, default is both.
This option runs pedstat only. This is good for testing your input files (family structures, etc.) and trait distributions.
Genotype error analysis.
Performs scan based on --error analysis. Error analysis must be done first. This option uses PedWipe program for zeroing out genotypes.
Set bits for Merlin analysis.
Specify missing value.
Genome-wide scan simulation.
Specify number of replicates for simulation. Default is 1.
Print AutoMerlin.sh help
Pedigree files (chr1.raw, chr2.raw, ..., chr22.raw), Map files (map1.dat, map2.dat, ... , map22.dat) and phenotype file phen.dat. See PedConvert documentation for file format.
Four (4) output files are created for each chromosome (example of chromosome 1):
All output files are moved to subfolder all_results.
Tero Hiekkalinna
Unpublished work, will be published by 2004