The diagram below, which inevitably appears somewhat confusing at first, provides an overview of the different files and programs used to organise and analyse pedigree data. You may only want to have a brief look at it at first, but you may find it helpful to refer back to later.
The files are generally referred to by their extensions, which in some cases are only a matter of convention. The central part of the process consists of the linkage analysis itself, which is carried out either by unknown and one of the other programs of the LINKAGE package (mlink, linkmap, lodscore or ilink), or by the vitesse program. This analysis requires a pedigree and locus data file as input, called pedfile.dat and datafile.dat respectively. Output is provided in files called outfile.dat and stream.dat or, in the case of vitesse, outfilev.dat and streamv.dat . Conventionally, and to support robust data management, the input files are converted from files with extension .par (for the locus data) and .ppd (for the pedigree data), while the output files are converted into files with extension .res and .out . This conversion process and the actual running of the analysis is performed by an MSDOS batch file (.bat) or Unix shell script (.sh), which also make use of a utility program called lsp. This batch or script file is produced by lcp or dolink. The lcp program needs to refer to the .ppd and .par files, whereas dolink reads the pedigree data from an .sdf file and the locus data from a file called locusdat.dat, and then writes its own .ppd and .par files in addition to the batch or script file. If lcp is used, the pedigree data will generally be stored in a simplified format with extension .ped , and this file will be converted to a .ppd file using the makeped program. (Sometimes the extensions .pre and .ped are used instead to refer to pre- and post- makeped files.)
In these exercises, all the pedigree data is stored in a database which is accessed by a program called qdb, the data being stored in files with extension .dbf and .hdc. Data can be exported from the database in a variety of formats using report files, which have extension .rep. As well as exporting data in the .sdf format which dolink requires, qdb is also used to produce files with extension .dat which can be read into the pedigree-drawing program, pedraw, although pedraw can also read .sdf, .ped and .ppd files directly.
The .out and .res files produced by the linkage analysis can be post-processed using the lrp or table utilities, which facilitate interpretation of the output in a variety of ways. The table program can be used to prepare data files for fastmap, and for the graphing programs gnuplot, easigraf and ACE/gr.
.hdc .dbf
| |
V V
QDB<---->.sdf
.rep--> | |
| \-----------------------\
V |
| V
| .dat
| |
| |
V |
.ped |
|| | | |
/-----------------------/| | V |
| /-------/ | |
| | | | \--------------------\ |
| | | V | |
| | | MAKEPED | |
| | | | | |
| V V V | |
| .par .ppd | |
| | | \--------------------\| |
|LCP/quiklink<---/----------/ | |
| | | | | |
| | ======================================== VVVV
V V | |<---LSP-->| | PEDRAW
========| V V |
| | datafile.dat pedfile.dat |
| .sh | | | | | |
========| | /--+---/ | |
| | | | V |
| | | \----\->UNKNOWN |
| | | | | |
| V V | V |
| VITESSE | ipedfile.dat, |
| | | | speedfile.dat |
| V | | | |
| outfilev.dat| V V |
| | V LINKAGE |
| | streamv.dat | | |
| | | V | |
| | | outfile.dat| |
| | | | V |
| /-------------/ stream.dat |
| | | | |
| | \-------------\ |
| | | |
========================================
| |
V V
.res .out
| |
V V
TABLE---\ LRP
| | | |
V | | V
.tab | | .txt
V V
.inp .plt, .gda
| |
V V
FASTMAP GNUPLOT
|
V
.out
Exercises in genetic linkage analysis
All material copyright (C) Dave Curtis 1996-2000
dcurtis@hgmp.mrc.ac.uk