*-----------------------------------------------------*
* TheSNPPit contributed script:                       *
* Parentage verification according to ICAR rules      *
*                                                     *
* Schwarzenbacher Hermann, ZuchtData GmbH, 22.08.2019 *
*-----------------------------------------------------*

*---------------------------------------------------------------------
* Purpose
*---------------------------------------------------------------------
   Example for snppit genotype import and export using a small test data set.
   Parentage verification and parentage discovery according to ICAR rules.
   You find a detailed description in
   https://www.icar.org/Documents/GenoEx/ICAR%20Guidelines%20for%20Parentage
   %20Verification%20and%20Parentage%20Discovery%20based%20on%20SNP.pdf


*---------------------------------------------------------------------
* Input
*---------------------------------------------------------------------
1. Genotype data
    PLINK .bed file format (https://www.cog-genomics.org/plink/1.9/input#bed)
    Data can be in any order with at least 196 ICAR recommeded SNP.
    If additionally 354 ICAR SNP for parentage discovery are delivered,
    then parentage detection is carried out as well.
    If more SNPs are delivered then SNP data will be filtered for relevant SNP.
    Sample IDs have to be provided for animal identification.

2. Pedigree data
    File in format: sample;animal;sire;dam;sex[1=male,2=female];birthdate[YYYY-MM-DD]
    Separator =';', with headers as given above.
    Pedigree should be provided for all animals in the genotype file.

3. Candidates for parentage verification and discovery with header "sample"
    Sample IDs are provided as animal identification.


*-----------------------------------------
*Output:
*-----------------------------------------
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     result.txt: 
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sample:                 Sample ID
animal:                 Animal ID
sire:                   Sire ID
dam:                    Dam ID
sex:                    Sex (1=male, 2=female)
birthdate:              format DD.MM.YYYY
UsableSNPAnimal:        No of usable parentage verification SNP for animal 
UsableSNPSire:          No of usable parentage verification SNP for sire
UsableSNPDam:           No of usable parentage verification SNP for dam
AnimalConclusion:       Outcome of call rate for animal
SireConclusion:         Outcome of parentage verification test for sire
DamConclusion:          Outcome of parentage verification test for dam
MatingConclusion:       Outcome of parentage verification test for sire & dam
SNPConflictsSire:       Number of genotype conflicts with sire
SNPConflictsDam:        Number of genotype conflicts with dam
SNPConflictsMating:     Number of genotype conflicts with sire and dam
UsableSNPDisAnimal:     No of usable parentage discovery SNP for animal 
UsableSNPDisSire:       No of usable parentage discovery SNP for sire
UsableSNPDisDam:        No of usable parentage discovery SNP for dam
UsableSNPDisParents:    No of usable parentage discovery SNP for sire & dam
PossSire:               Possible sire
PossSireConclusion:     Outcome of parentage discovery test for sire
PossDam:                Possible dam
PossDamConclusion:      Outcome of parentage discovery test for dam
PossParentsConclusion:  Outcome of parentage discovery test for sire and dam
SNPDisConflictsSire:    Number of genotype conflicts with possible sire
SNPDisConflictsDam:     Number of genotype conflicts with possible dam
SNPDisConflictsParents: Number of genotype conflicts with possible sire and dam
Date:                   Date of analysis