Pedcheck program is used to check pedigree file for detecting marker typing incompatibilities in pedigree data.
Command is:
pedcheck
Pedcheck command line options are:
% pedcheck -h
PedCheck 1.1 (c) Jeff O'Connell 1997,1999 University of Pittsburgh
Last revision: November 24, 1998
Date: Tue May 27 11:36:23 2003
*****************************************************************
* PedCheck is now covered by a license agreement. *
* The use of this software may require a fee. *
* Details can be found on the web site: *
* http://watson.hgen.pitt.edu. *
* This copy of PedCheck expires on January 15, 2004. *
*****************************************************************
PedCheck options:
-p pedigree file ; default: pedfile.dat
-d locus file ; default: datafile.dat
-n names file
:-e :use estimated allele frequencies; default:use datafile frequencies if available, else set equal.
-a :create list of estimated allele frequencies based
on allele counting across all pedigrees; default: false.
-m : pre makeped format (NO LONGER NEEDED)
-z : create a Mendelian consistent pedigree by zeroing out
all individuals at any marker in a pedigree that has an
error. Put comments at the beginning the file. Output file
is zeroout.dat.
-c :same as -z except comments are put into the file comment.dat
-t : use the Ped and Per name from pre-makeped format;
default: use the labels from post-makeped format.
-x : X-linked data
-i : print intro header; default: false
-2 : Level 2 checking ; default: Level 0 and Level 1
-3 : Level 3 checking ; default: Level 0 and Level 1
See README file for explanation. -4 : Level 4 checking ; default: Level 0 and Level 1
%
Pedcheck can automatically detect pedigree file format (pre-makeped or post-makeped (LINKAGE)).
Example: Let's assume that we have following (pre-makeped format) pedigree file (ped.pre), with one mendelian
incompability in second marker, family ped2 between mother and son1:
ped1 father 0 0 1 2 1 2 0 0
ped1 mother 0 0 2 1 1 1 0 0
ped1 son1 father mother 1 2 1 2 0 0
ped1 son2 father mother 1 1 1 1 0 0
ped1 dau1 father mother 2 2 1 2 1 1
ped1 dau2 father mother 2 1 1 1 4 5
ped2 father 0 0 1 2 1 3 2 4
ped2 mother 0 0 2 1 1 3 2 3
ped2 son1 father mother 1 2 3 3 4 4
and let's make names file (names.dat) which contains names of the markers, in first line X means that trait locus (disease) will skipped:
X
Marker1
Marker2
And then let's run pedcheck with following command line arguments:
pedcheck -p ped.pre -n names.dat
Pedcheck output to screen is here and it created output file pedcheck.err. Pedcheck has four different levels for checking mendelian incompatibilities and those can be defined in command line.
Example of running full check (level -4) for LINKAGE format pedigree and locus file:
pedcheck -4 -p pedin.dat -d datain.dat
Jeff O'Connell. Copyright: (c) Jeff O'Connell 1997 , University of Pittsburgh
PedCheck: A program for identifying genotype incompatibilities in linkage analysis: O'Connell JR, Weeks DE, Am J Hum Genet 1998 Jul;63(1):259-66