My goal is to convert Illumina data to forward/reverse strand data (AffyMetrix). I have 10K, 60K, 80K and 660K data from both sources.

I have the following types of files:

***.ref
snp CHROMOSOME POSITION COUNT_ALLELE OTHER_ALLELE
snp1 17 190170 G A
snp2 17 469495 A G
--- One line for each SNP


***.dat
pig_id snp1 snp2 snp3 snp4 --- snp58448
11641206 1 0 1 0 0 
11324561 1 0 2 0 0 
14561322 2 1 1 0 1 
13513507 0 0 2 0 0 
--One line per animal, one row per snp

I also have an Illumina HD annotation file which looks as follows:

Illumina     Inc.                                                                   
[Heading]                                                                       
Descriptor File Name    GGP HD Porcine.csv                                                                  
Assay Format    Infinium HD Ultra                                                                   
Date Manufactured   5/15/2013                                                                   
Loci Count  68516                                                                   
[Assay]                                                                     
IlmnID  Name    IlmnStrand  SNP AddressA_ID AlleleA_ProbeSeq    AddressB_ID AlleleB_ProbeSeq    GenomeBuild Chr MapInfo Ploidy  Species Source  SourceVersion   SourceStrand    SourceSeq   TopGenomicSeq   BeadSetID
LD-Porcine80K_ALGA0000022-0_T_F_2164561890-0_T_F_2165597341 ALGA0000022 TOP [A/G]   19808437 *seq*     10.2 1   865364  diploid Sus scrofa  rs80958395  0   TOP *seq*    [A/G]877

When I compare SNPs from the illumina annotation file with the affymetrix annotation file, I find inconsistency in the SNP callings.
For example after manually checking some values I find the following:
sometimes illumina TOP A/G is called as T/C in affymetrix, it sometimes is also called as A/G in affymetrix.
sometimes illumina TOP A/C is (sometimes?)called as T/G in affymetrix,
sometimes illumina BOT T/G is (sometimes?)called as A/C in affymetrix

I hope somebody will be able to help me out here