Welcome to SPLITPED

S. J. Quinn Last updated 21/8/06

What is SPLITPED?

SPLITPED is a software package with two functions. It will:

(a) take any pedigree file and split the pedigree into sub-pedigrees to allow you to analyze these files using your preferred package. Each sub-pedigree is induced by taking a pair of cases, their first degree relatives, the ancestors that connect these cases, up to the nearest common pair of ancestors, and any other ancestors contained in loops that affect IBD sharing.
(b) split the pedigree into sub-pedigree, and compute S-pairs statistics for each sub pedigree file using MERLIN's "--ibd" option. It then sums these statistics to obtain an approximate S-pairs statistic for the pedigree as a whole.

How do I install SPLITPED?

Copy the PERL file " splitped.pl " (right click --> "Save Link as") onto your working directory if you are using option (a) only. If you are using option (b), then you will also need to copy and compile the FORTRAN file " simulator.f "(right click --> "Save Link as").

How do I use SPLITPED?

If you just want to split a pedigree file (for example, a pedigree file called "family.ped" into sub-pedigrees, then type:

perl splitped.pl family.ped

Splitped will produce sub-pedigree files for each case pair, for example, family.ped_12_14 (corresponding to the sub-pedigree for persons 12 and 14). Additionally, there is a summary file, called "subpedigrees.txt" that lists each case pair and the people that comprise the induced sub-pedigree.
If you want to analyze the data in your pedigree using SPLITPED type in the command "perl splitped.pl followed by the arguments that you would type if you were using MERLIN (MERLIN is available at http://www.sph.umich.edu/csg/abecasis/Merlin/tour/ . and this option assumes that you are familiar with MERLIN.).

That is, instead of typing

merlin.pl -p family.ped -m family.map -d family.dat --markerNames --ibd

you type

perl splitped.pl -p family.ped -m family.map -d family.dat --markerNames --ibd

Two files are produced: a text file called "splitped.ibd" that contains the S-pairs statistics for each marker and case pair, the approximate S-pairs statistic for the overall pedigree and empirical p values that correspond to this statistic at each marker; and the text file "subpedigrees.txt" as described above.

A SPLITPED example.

The following files are provided to allow you to verify that you using the program as intended

Option 1

Copy the ped, map and dat files example.ped, example.map and example.dat. To split the pedigree file into sub-pedigrees type

perl splitped.pl -p example.ped

You should see in your directory 6 sub pedigree files, example.ped_1_2, example.ped_1_3, example.ped_1_4, example.ped_2_3, example.ped_2_4, example.ped_3_4, together with the summary file: subpedigrees.txt

Option 2

To analyse the data, type

perl splitped.pl -p example.ped -m example.map -d example.dat --ibd

You should see the files splitped.ibd and subpedigrees.txt in your directory. You could, of course, have added any other options that MERLIN supports (in conjunction with -ibd), such as -grid 0.5, -start -10, --stop 20, --cluster etc.

Please forward any queries to: Stephen.Quinn@utas.edu.au