An original copy of PEDSTATS downloaded from:
https://csg.sph.umich.edu/abecasis/PedStats/download/pedstats-0.6.12.tar.gz
PEDSTATS
(c) 2000 - 2005 Goncalo Abecasis, portions (c) 2002-2005 Jan Wigginton
This document contains two sections: RESTRICTIONS ON USE and BRIEF
INSTRUCTIONS.
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RESTRICTIONS FOR USE OF THIS VERSION
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DISCLAIMER
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This version of PEDSTATS is provided to you free of charge. It comes with
no guarantees. If you report bugs and provide helpful comments, the next
version will be better.
DISTRIBUTION
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The latest version of PEDSTATS is always available at:
http://www.sph.umich.edu/csg/abecasis/Pedstats
If you use PEDSTATS please register by e-mailing wiggie@umich.edu or filling
out the web registration form. Redistribution of PEDSTATS in source or compiled
formats is not allowed.
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COMPILING AND INSTALLING PEDSTATS
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Type make and follow instructions.
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START OF BRIEF INSTRUCTIONS
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A more detailed tutorial is available on the web at:
http://www.sph.umich.edu/csg/abecasis/Pedstats/tour
A summary reference for all Pedstats options is available at:
http://www.sph.umich.edu/csg/abecasis/Pedstats/reference.html
INPUT FILES
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Pedigree and data files can be in linkage or QTDT format. For detailed
descriptions of these formats see http://www.well.ox.ac.uk/asthma/QTDT
and http://linkage.rockefeller.edu.
To specify input files use:
>pedstats -d datafile -p pedfile
To specify an ibd file (necessary only if you want to see ibd output).
> pedstats -d datafile -p pedfile -i ibdfile
OUTPUT OPTIONS
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Default output is in text format. Graphical output in PDF format can
be requested by using the --pdf command line option. Default PDF out
file name is ped_summary.pdf. To send pdf output to another file, do so
using the -a command line option.
> pedstats -d datafile -p pedfile --pdf -a pdffile
BASIC ANALYSES
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Basic analysis can be requested on the command line, and include
pairwise statistics (--pairs), hardy-weinberg equilibrium testing
using all pedigree data (--checkAll), a selection of unrelated individuals
(--checkUnrelated), using just founders (--checkFounders) or
an unrelated sample and all individuals (--hardyWeinberg).
Counts at each marker locus of families
with ibd information specified in the ibd file can be obtained using the (--ibd)
option
MENDELIAN INHERITANCE CHECKS
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By default. To turn off use --ignoreMendelianErrors
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REFERENCE
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Wigginton JE and Abecasis GR (2005) PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping
data Bioinformatics 21:3445 - 3447
Jan Wigginton
wiggie@umich.edu