[BioC] SNP6 data to VCF

[Sean Davis]

On Mon, Feb 13, 2012 at 2:28 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
>
>
> On Mon, Feb 13, 2012 at 2:13 PM, Sean Davis <sdavis2 at 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 at 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

Told you I was rusty.  Thanks, Vince.

Sean


>>
>> 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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>
>