Calculate the pairwise IBD/IBS metrics - Part I (--genome)

[davidonlaptop]

Description

Similar to plink --genome option. See the wiki on IBS-MDS Process and the diagram for the Genome file.

The input files are those created in #2.

The fields required for --cluster and --mds-plot are:

• FID1: family ID of individual 1
• IID1: individual ID of individual 1
• FID2: family ID of individual 2
• IID2: individual ID of individual 2
• DST: IBS distance
• PPC: IBS binomial test

There is more fields, but they are will be done in Part II.

Analysis

Add a comment to this issue with:

• plink version used as reference (1.07 or 1.90 beta 3)
• relevant C++ function name(s) and the file name(s) where they appear
• Document the algorithm and/or mathematical formula to compute the fields:
  • DST
  • PPC
  • any other field required as a dependency

    Design

Add a comment to this issue describing how this will be implemented in Spark, and how it differs from plink.

Also update the class diagram on the wiki page describing PLink formats (when incomplete) and add a class diagram describing the models implemented in Scala for this feature on the wiki page on the MGL804 formats.

Implementation

The implementation should use:

• Scala
• Spark RDD
• Spark MLlib / GraphX (if appropriate)

Important note: The model can be only in memory for now, but you'll need to integrate into the ADAM format later on. You'll probably need to create a new record type.

[iki-v]

Informations pouvant être utiles

Visualisation de contenu dans le fichier .bed : $ xxd -b test.bed

Fonctions : calc_genome_emitn

[iki-v]

Bonjour, pourriez-vous faire un statut sur ce point ?

[sfcwallace]

Voici le lien vers la page du Wiki décrivant les champs du fichier .genome: https://github.com/GELOG/adam-ibs/wiki/Algorithm-for-Pairwise--IBS-IBD-computation-(--genome)