Thanks for your help Tim and Herve.

It would be very useful to include the SNPs that have a value for the
chr-pos field even if they have more than 1 CTG line for my purposes since
I deal with a lot of immune-related genes that tend to be difficult to
map.  Would it be possible to include these types of SNPs, but flag them as
having more than 1 CTG line?

Thanks for your help,
Christina


On Tue, Jan 15, 2013 at 11:00 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Christina,
>
> According to the official announcement:
>
>
> http://www.ncbi.nlm.nih.gov/**mailman/pipermail/dbsnp-**
> announce/2012q2/000122.html<http://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2012q2/000122.html>
>
> there are 53,558,214 rs ids in dbSNP 137 for Human.
>
> But in SNPlocs.Hsapiens.dbSNP.**20120608:
>
>   > library(SNPlocs.Hsapiens.**dbSNP.20120608)
>   > sum(getSNPcount())
>   [1] 45416711
>
> As explained in ?SNPlocs.Hsapiens.dbSNP.**20120608, the package (like
> all other SNPlocs packages) was curated:
>
>      SNPs from dbSNP were filtered to keep only those satisfying the 3
>      following criteria:
>
>         • The SNP is a single-base substitution i.e. its type is "snp".
>           Other types used by dbSNP are: "in-del", "mixed",
>           "microsatellite", "named-locus",
>           "multinucleotide-polymorphism"**, etc... All those SNPs were
>           dropped.
>
>         • The SNP is marked as notwithdrawn.
>
>         • A *single* location on the reference genome (GRCh37.p5) is
>           reported for the SNP, and this location is on chromosomes
>           1-22, X, Y, MT.
>
> In the case of rs7775397, it was dropped because of this last reason.
> More precisely, the record in ds_flat_ch6.flat for this SNP contains
> the following CTG lines:
>
> CTG | assembly=GRCh37.p5 | chr=6 | chr-pos=32261252 | NT_007592.15 |
> ctg-start=32201252 | ctg-end=32201252 | loctype=2 | orient=+
> CTG | assembly=GRCh37.p5 | chr=6 | chr-pos=? | NT_113891.2 |
> ctg-start=3732030 | ctg-end=3732030 | loctype=2 | orient=+
> CTG | assembly=GRCh37.p5 | chr=6 | chr-pos=? | NT_167245.1 |
> ctg-start=3540499 | ctg-end=3540499 | loctype=2 | orient=+
> CTG | assembly=GRCh37.p5 | chr=6 | chr-pos=? | NT_167246.1 |
> ctg-start=3604088 | ctg-end=3604088 | loctype=2 | orient=+
> CTG | assembly=GRCh37.p5 | chr=6 | chr-pos=? | NT_167248.1 |
> ctg-start=3522471 | ctg-end=3522471 | loctype=2 | orient=+
> CTG | assembly=GRCh37.p5 | chr=6 | chr-pos=? | NT_167249.1 |
> ctg-start=3609047 | ctg-end=3609047 | loctype=2 | orient=+
>
> That is, more than 1 CTG line corresponding to the reference assembly
> (GRCh37.p5). This is the reason why the SNP was dropped.
>
> I realize now that maybe I could keep those SNPs that have more than
> 1 CTG line corresponding to the reference assembly as long as exactly
> 1 of them actually provides a value for the chr-pos field. Would that
> be reasonable?
>
> Thanks,
> H.
>
>
>
> On 01/15/2013 05:19 PM, Christina Chaivorapol wrote:
>
>> Hi,
>>
>> Has anyone ever had a case where a SNP was not found in
>> SNPlocs.Hsapiens.dbSNP.
>> 20120608, but is found in dbSNP 137?  I am having this problem with SNP
>> rs7775397.
>>
>>  library(SNPlocs.Hsapiens.**dbSNP.20120608)
>>> rsidsToGRanges('rs7775397')
>>>
>> Error in .snpid2rowidx(x, snpid) : SNP id(s) not found: 7775397
>>
>> Thanks,
>> Christina
>>
>>  sessionInfo()
>>>
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=C                 LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] datasets  utils     grDevices graphics  stats     methods   base
>>
>> other attached packages:
>> [1] SNPlocs.Hsapiens.dbSNP.
>> 20120608_0.99.8
>> [2] BSgenome_1.26.1
>> [3] Biostrings_2.26.2
>> [4] GenomicRanges_1.10.5
>> [5] IRanges_1.16.4
>> [6] BiocGenerics_0.4.0
>>
>> loaded via a namespace (and not attached):
>> [1] parallel_2.15.2 stats4_2.15.2
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Christina Chaivorapol, Ph.D.
Genentech, Inc.
Bioinformatics & Computational Biology
phone: 650-225-6903
chrichai@gene.com

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