96
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Download
=== Required Input Files ===
=== Required Input Files ===
==== Pedigree file (.ped) ====
==== Pedigree file (.ped) ====
File fed to -ped option, in [[Merlin]] format pedigree file. For details of the Merlin file format, see the Merlin tutorial [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html]. <br>
File fed to -ped option, in [[Merlin]] format pedigree file. For details of the Merlin file format, see the Merlin tutorial [http://csg.sph.umich.edu//abecasis/Merlin/tour/input_files.html]. <br>
Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele). <br>
Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele). <br>
==== Marker information (.dat) file ====
==== Marker information (.dat) file ====
File fed to -dat option, in [[Merlin]] format marker information file. For details of the Merlin file format, see the Merlin tutorial [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html]. <br>
File fed to -dat option, in [[Merlin]] format marker information file. For details of the Merlin file format, see the Merlin tutorial [http://csg.sph.umich.edu//abecasis/Merlin/tour/input_files.html]. <br>
=== Optional Input Files ===
=== Optional Input Files ===
splitPed.pl -ped example.ped -dat example.dat -map example.map -windowLength 10000000 -overlapLength 1000000 -o split
splitPed.pl -ped example.ped -dat example.dat -map example.map -windowLength 10000000 -overlapLength 1000000 -o split
splitPed.pl -ped example.ped -dat example.dat -map example.map -windowLength 10000000 -overlapLength 1000000 -splitPed 1 -o split.with_ped
splitPed.pl -ped example.ped -dat example.dat -map example.map -windowLength 10000000 -overlapLength 1000000 -splitPed 1 -o split.with_ped
splitPed.pl -ped example.ped -dat example.dat -windowSize 10000 -overlapSize 1000 -o split
splitPed.pl -ped example.ped -dat example.dat -nWindows 12 -overlapSize 1000 -o split
== Download ==
You can download splitPed at [http://csg.sph.umich.edu//yli/splitPed/download/ splitPed Download Page].
== Questions and Comments? ==
== Questions and Comments? ==
Email [mailto:yunli@med.unc.edu Yun Li].
Email [mailto:yunli@med.unc.edu Yun Li].
