Changes

== Input files ==

== Input files ==

Required input files are -p input.ped -d input.dat -g glfIndex files

Required input files are -p input.ped -d input.dat file to specify the relationship, and either -g input.gif or --in_vcf input.vcf to specify sequence data.

* An example in.ped file looks like the following:

* An example in.ped file looks like the following (for more info refer to the merlin documentation):

  fam1 p1  0  0  1  1

  fam1 p1  0  0  1  1

  fam1 p2  0  0  2  2

  fam1 p2  0  0  2  2

  T GLF_Index

  T GLF_Index

* An example glfIndex file is like the following and the numbers (except zeros) in the 6th column in the above in.ped file have to be present in the first column.

In the above .dat file, it specifies the GLF_Index for the 6th column in the .ped file. If -g input.gif is specified, then the input.gif looks like the following, where the numbers (except zeros) in the 6th column in the above input.ped file have to be present in the first column.

 

  1  /home/me/sample1.glf

  1  /home/me/sample1.glf

  2  /home/me/sample2.glf

  2  /home/me/sample2.glf