IBS-IBD Estimation

[davidonlaptop]

Description

This feature adds the --rel-check, --min, --max, --het, --indep, --indep-pairwise, --homozyg, --homozyg-snp, --homozyg-kb, --homozyg-window-het, --homozyg-window-missing, --homozyg-window-threshold, --homozyg-density, --homozyg-gap, --homozyg-group, --pool-size, --homozyg-match, --consensus-match, --homozyg-verbose, --ibs-test, --segment, --all-pairs, --segment-length, --segment-snp, --segment-group, --segment-verbose, --mperm option(s) based on the input file described in #3.

This feature also generates the following file formats: HET, HOM, HOM.OVERLAP, SEGMENT, SEGMENT.SUMMARY, SEGMENT.SUMMARY.MPERM.For more info, check: http://pngu.mgh.harvard.edu/~purcell/plink/ibdibs.shtml

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 structure of all file format(s) described above generated by plink.
• Document the algorithm and/or mathematical formula to compute all the missing fields described above:

  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 integrates with the models implemented in scala by this project and use:

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