[BioC] SNP6 data to VCF

[Sean Davis]

Hi, all.

I'm a little rusty on my oligo array software tools.  I'm interested
in taking Affymetrix SNP6 data to VCF format.  To do that, I am going
to need to:

1.  Call SNPs
2.  Determine strand and reference allele for each SNP on the array
3.  Assign the correct alleles to each SNP for each sample
4.  Write out the VCF file with the correct genotypes (on the positive
strand, reference allele correctly specified)

What is the best way to do steps 1-3?  I'll deal with step 4 since I
don't think that has been implemented directly.

Thanks,
Sean