Mega2 is menu-based program for converting LINKAGE format pedigree (pedin.dat), locus file (datain.dat) or names file (see Mega2 doc) and map file (map.dat) to different input file formats used by Simwalk2 and others.
Command is:
mega2
Mega2 can convert files to many formats, here is the list:
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ANALYSIS MENU
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1 SimWalk2-format 14 SAGE-format
2 MENDEL-format 15 TDTMax analyses
3 ASPEX-format 16 SOLAR-format
4 GeneHunter-Plus format 17 Vitesse-format
5 GeneHunter format 18 Linkage-format
6 APM-format 19 Test loci for HWE
7 APM MULT format 20 Allegro-format
8 Create nuclear families 21 MLBQTL format
9 SLINK-format 22 SAGE 4.0 format
10 SPLINK-format 23 Pre-makeped format
11 Homogeneity analyses 24 Merlin/SimWalk2-NPL format
12 SIMULATE-format 25 PREST format
13 Create summary files 26 PAP format
Example: Let's assume that follwing input files are in directory: LINKAGE pedigree file pedin.01, LINKAGE locus file datain.01 and map file map.01. File extension 01 means that data is from chromosome 1 and mega2 automatically detects input files.
Step-by-step Simwalk2 conversion (parametric linkage analysis):
% mega2
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MEGA2
Version 2.3
by Daniel E. Weeks, Nandita Mukhopadhyay, Lee W. Almasy,
and William Mullvihill
Based on CHAPM, which was coded by Mark Schroeder
Copyright (c) 1997-2003 The University of Pittsburgh
Last updated: Jun 13 2002, 15:28:32
This version is valid until June 15, 2003.
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Moved existing MEGA2.BATCH to MEGA2.BATCH.old
Moved existing MEGA2.LOG to MEGA2.LOG.old
Moved existing MEGA2.KEYS to MEGA2.KEYS.old
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Mega2 input menu:
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0) Done with this menu - please proceed
1) Chromosome number: 1
2) Input file extension: 01
3) Locus datafile: datain.01
4) Pedigree datafile: pedin.01
5) Map datafile: map.01
6) Omit datafile (optional): _
7) Include all pedigrees whether typed or not
8) Set up for simluating genotyping errors: [no ]
Select from options 0-8 (8 to toggle) >
Comment: mega2 automatically detects input files. If something needs to be changed type corresponding number, press enter and edit. But now we are ready to proceed, let's select 0.
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ANALYSIS MENU
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1 SimWalk2-format 14 SAGE-format
2 MENDEL-format 15 TDTMax analyses
3 ASPEX-format 16 SOLAR-format
4 GeneHunter-Plus format 17 Vitesse-format
5 GeneHunter format 18 Linkage-format
6 APM-format 19 Test loci for HWE
7 APM MULT format 20 Allegro-format
8 Create nuclear families 21 MLBQTL format
9 SLINK-format 22 SAGE 4.0 format
10 SPLINK-format 23 Pre-makeped format
11 Homogeneity analyses 24 Merlin/SimWalk2-NPL format
12 SIMULATE-format 25 PREST format
13 Create summary files 26 PAP format
Select an option between 1-26 >
Comment: Let's select Simwalk2-format: 1.
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You have selected: SimWalk2-format
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SimWalk2 program options:
1) Haplotype analysis
2) Parametric Linkage analysis
3) Non-Parametric Linkage analysis
4) IBD analysis
5) Mistyping analysis
Enter selection 1-5 >
Comment: We wanted parametric linkage analysis: 2
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Analysis option: Simwalk2-Parametric Linkage.
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Checking format of pedigree file pedin.01.
Pedigree file pedin.01 is in post-makeped format.
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Data read in from Locus file:
Total number of loci = 3, number of marker loci = 2
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Data read in from pedigree file:
Marker Genotypes
Pedigree-type Pedigrees People Males Females Typed Total
Post-makeped 40 840 480 360 1680 1680
Pedigrees Pedigrees Males Males Females Females
Typed Untyped Typed Untyped Typed Untyped
40 0 480 0 360 0
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Data read in from map file.
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LOCUS REORDERING MENU
1) Select all loci in map order on chromosome: 1
2) Select by locus number.
3) Select one chromosome and select loci on it.
4) Select one or more chromosomes and select loci on them.
Enter 1, 2, 3 or 4 >
Comment: Mega2 displays some summary information and we proceed to all loci: 1
Found 1 trait locus:
1 Affection status locus: TRAIT
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Found one trait locus TRAIT
Simwalk2-Parametric Linkage requires at least one trait, selecting this locus for analysis.
Found 1 trait locus:
1 Affection status locus: TRAIT
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Converting to pedigree tree ...
Checking locus integrity...
Done checking locus integrity.
Checking pedigree integrity...
Done checking pedigree integrity.
Pedigree statistics after selecting chromosomes and marker loci:
Marker Genotypes
Pedigrees People Males Females Typed Total
40 840 480 360 1680 1680
Pedigrees Pedigrees Males Males Females Females
Typed Untyped Typed Untyped Typed Untyped
40 0 480 0 360 0
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SimWalk2 file name menu
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0) Done with this menu - please proceed
1) Locus file name : LOCUS.01 [overwrite]
2) Pedigree filename : PEDIGREE.01 [overwrite]
3) Penetrance file name : PEN.01 [overwrite]
4) Batch file name : BATCH2.01 [overwrite]
5) C-shell file name : loc.01.sh [overwrite]
6) Take person ids from input
pedigree record field(if given): "Per" field
Select options 0-5 to enter new file names,
6 to toggle >
Comment: Converting and info about output files, select 0
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Mega2 created the following files for Simwalk2-Parametric Linkage:
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Locus file: LOCUS.01
Pedigree file: PEDIGREE.01
Penetrance file: PEN.01
Simwalk2 batch file: BATCH2.01
C-Shell script: loc.01.sh
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For more information on this run, see the following files:
MEGA2.LOG
MEGA2.KEYS
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If you use Mega2 as part of a published work, please reference
Mega2 by citing this abstract:
Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (1999)
Mega2, a data-handling program for facilitating genetic linkage
and association analyses. Am J Hum Genet 65:A436.
as well as citing the web site and the version that you used.
For example, the web site citation for version 2.3 should be:
Mukhopadhyay N, Almasy L,Schroeder M, Mulvihill WP,
Weeks DE (2002) Version 2.3 http://watson.hgen.pitt.edu
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Comment: mega2 summary message.
Mega2 converted files and created C-shell script named as loc.01.sh, which is simple script to run Simwalk2 with just converted input files. To start analysis type:
sh loc.01.sh
Script name is different when some other analysis option from Simwalk2 is chosen.
Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill, Daniel E. Weeks. Copyright © 1999-2002 by the University of Pittsburgh
If you use Mega2 as part of a published work, please remember to reference Mega2. You may reference it by citing this abstract:
Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (1999) Mega2, a data-handling program for facilitating genetic linkage and association analyses. Am J Hum Genet 65:A436
as well as citing the web site and the version that you used. The web site citation for version 2.3 should be:
Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (2001) Mega2 (Version 2.3). http://watson.hgen.pitt.edu