Tehdyt toimenpiteet
PedCheck
Version
V.1.1 installed in HIPPU
V.1.1 installed in MURSKA
Description
PedCheck detects marker typing incompatibilities in pedigree data -- if they are Mendelian consistent.
Usage
The program is installed in HIPPU (hippu.csc.fi) and in MURSKA (murska.csc.fi).
The software needs to be initialized before use:
module load pedcheck
to run PedCheck, type:
pedcheck
run also
pedcheck -2
to guarantee that there is no inconsistency in a pedigree (see the documentation).
Input files:
PedCheck will look for 'datafile.dat' and 'pedfile.dat' as default inputs. These are LINKAGE format files ( which means that makeped has been run on the pedigree file ). If either of these is not found, PedCheck will prompt you to input a file name.
Command line options are also available for inputing these files: -p -d .
PedCheck can handle pre-makeped files, so the pedigree and individual names can be any string, not just numeric.
Documentation
On-line documentation is available at the authors web page.
References
If you use PedCheck in any published work, please cite:"PedCheck: A program for identifying genotype incompatibilities in linkage analysis," O'Connell JR, Weeks DE, Am J Hum Genet 63:259-266
User support
| Saren Ari-Matti | +358 9 457 2282 | Ari-Matti.Saren at csc.fi |
