On Mon, Feb 13, 2012 at 2:13 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> 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
>

for 2 and 3 pd.genomewidesnp.6 has the metadata

> con  = pd.genomewidesnp.6@getdb()
> dbListTables(con)
 [1] "featureSet"        "featureSetCNV"     "fragmentLength"
 [4] "fragmentLengthCNV" "pmfeature"         "pmfeatureCNV"
 [7] "sequence"          "sequenceCNV"       "sqlite_stat1"
[10] "table_info"

> ss = dbGetQuery(con, "select * from featureSet limit 5")
> ss
  fsetid    man_fsetid affy_snp_id dbsnp_rs_id chrom physical_pos strand
1      1 SNP_A-2131660          NA   rs2887286     1      1156131      0
2      2 SNP_A-1967418          NA   rs1496555     1      2234251      0
3      3 SNP_A-1969580          NA  rs41477744     1      2329564      0
4      4 SNP_A-4263484          NA   rs3890745     1      2553624      0
5      5 SNP_A-1978185          NA  rs10492936     1      2936870      1
  cytoband allele_a allele_b
1   p36.33        C        T
2   p36.33        A        G
3   p36.32        A        G
4   p36.32        C        T
5   p36.32        C        T



> 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
>
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