PedConvert

Description

Program combines and converts pre-makeped LINKAGE pedigree file, phenotype file and MEGA2 format map file to MERLIN format. PedConvert is fast, it uses Red-Black Tree data structures.

Usage

Command is:

   pedconvert

Pedconvert has following command line arguments:

   % pedconvert
   -------------------------------------------------------------------------------
                   Program PedConvert 1.2 - 18th of June 2004                     
          Copyright (C) 2004 Tero Hiekkalinna, Tero.Hiekkalinna@Helsinki.FI       
           Program for converting genotype/phenotype data to MERLIN format        
           Program uses Red-Black-Tree data structures for Fast conversion        
   -------------------------------------------------------------------------------
    
   Usage: pedconvert  [options]
    
          -p    pedigree  file
          -f    phenotype file
          -m    map file
          -n    number of markers in pedigree file
          -t    pedigree file has dicotomous trait as first phenotype and
                it will be read and ignored
          -s    add SEX as covariate
          -a    Set all phenotypes in phenotype file to traits. This can be used
                if multiple traits are being anayzed at same Merlin run
          -only [males,females]
    
   Example: pedconvert -p chr1.ped -f phen.dat -m map1.dat -n 78
   %

Command line options

Options -p, -f, -m and -n are mandatory!

-p

Specify pedigree file name.

-f

Specify phenotype file name.

-m

Specify map file name.

-n [number]

Specify number of markers in pedigree file.

-t

pedigree file has dicotomous trait as first phenotype and it will be read and ignored.

-s

Add SEX as covariate.

-a

Set all phenotypes in phenotype file to traits. This can be used if multiple traits are being anayzed at same Merlin run. By default first phenotype in phenotype file is used as TRAIT and rest of the phenotypes are set to covariates.

-only [males,females]

If you want to do sex spesific males/females analysis only, use option -only males to select MALE phenotypes and -only females to select FEMALES phenotypes.

Example input/output files

Phenotype file format:

Columns are: pedigree ID, person ID, Phenotype(s). First line includes number of phenotypes and phenotype names.

    1    Phen_1
    1  1  1.54
    1  3  1.44
    2  2  1.98
    2  3  1.39

If you want to use covariates in variance component analysis, list them after first phenotype (missing value is x):

    2    Phen_1   Phen_2
    1  1  1.54  34
    1  3  1.44  45
    2  2  1.98   x
    2  3  1.39  56

Pedigree and person number have to correspond to ids in pedigree file!

Pedigree file format:

Pedigree files are pre-makeped format (see Pedigree file format documentation!). Pedigree file can include dicotomous trait column (as first phenotype!), but that infomation must be given to PedConvert with option -t.

Map file format:

Map file must be in MEGA2 format (see Map file format documentation).

Example input files:

• Pedigree file (includes dicotomous trait column!): chr1.raw
• Phenotype file: phen.dat
• Map file: map1.dat

Let's run PedConvert with following options:

   pedconvert -p chr1.raw -f phen.dat -m map1.dat -n 2 -t

Output files:

• Merlin pedigree file: merlin.ped
• Merlin locus file: merlin.dat
• Merlin map file: merlin.map

Let's run PedConvert with following options, sex as covariate!:

   pedconvert -p chr1.raw -f phen.dat -m map1.dat -n 2 -t -s

• Merlin pedigree file: merlin.ped
• Merlin locus file: merlin.dat

Let's run PedConvert with following options, only males!:

   pedconvert -p chr1.raw -f phen.dat -m map1.dat -n 2 -t -only males

• Merlin pedigree file: merlin.ped
• Merlin locus file: merlin.dat

References

Unpublished work, will be published by 2004

Author

Tero Hiekkalinna