Hello UCSC,
I would appreciate if you can provide me some help... I have some problems
trying to get the correct information on minor allele frequency.
If I understand correctly
* Common SNPs (132): uniquely mapped variants that appear in at least 1% of
the population
* Flagged SNPs (132): uniquely mapped variants, excluding Common SNPs, that
have been flagged by dbSNP as "clinically associated"
* Mult. SNPs (132): variants that have been mapped to more than one genomic
location
* Common SNPs (132) and Flagged SNPs (132) should be mutually exclusive
that is as "clinically associated" SNPs are not "common" and common SNPs are
not flagged as "clinically associated". But when I download the information
for rs169547 (only as an example) I went through the Table browser and I choose
CommonSNP(132),
http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&position=chr13:32929380-32929390&hgsid=193533287
* I get the results that I send you in the attached file..
* This SNP is flagged as clinically associated....why? I downloaded through
the common SNPs?
* Then I get 3 frequencies for 3 alleles: G,A,C,
0.963316,0.033403,0.003281,
* Is the minor allele freq 0.003281? for C?
However in db132
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs169547
this SNP has a MAF/MinorAlleleCount: T=0.025/32 and for T. Is the minor allele
T or C?
Am I looking at the wrong columns? I would appreciate if you can help me to get
into the right track...
Thanks
Kind regards /Teresita
Teresita Díaz de Ståhl, PhD., Assoc. Prof.
Department of Oncology-Pathology
Cancer Center Karolinska, CCK R8:04
Karolinska Institutet
SE-171 76 Stockholm, Sweden
+46-8-517 721 35 (office)
E-mail: [email protected]
-----Original Message-----
From: Brooke Rhead [mailto:[email protected]]
Sent: den 28 april 2011 01:29
To: Teresita Diaz De Ståhl
Cc: [email protected]
Subject: Re: [Genome] minor allele frequency
Hello Teresita,
Allele frequencies are now included in our SNP tables (this was not true prior
to dbSNP build 132). So, if you download the snp132 table from here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
(the filename is snp132.txt.gz), you will get allele frequencies. Note that
this file is quite large, so you will probably want to use one of the alternate
methods for downloading described at the top of that page.
The table schema is shown here:
http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=snp132&hgta_table=snp132&hgta_doSchema=describe+table+schema
Note that not all SNPs include allele frequency data.
You might also be interested to know that we now provide 4 separate SNP tracks,
described in our announcement here:
http://genome.ucsc.edu/goldenPath/newsarch.html#041811.2
(and also described on the SNP track descriptions in the Genome Browser).
If you have further questions, please feel free to contact us again at
[email protected]<mailto:[email protected]>.
--
Brooke Rhead
UCSC Genome Bioinformatics Group
On 04/27/11 07:41, Teresita Diaz De Ståhl wrote:
> Hi,
>
> I wonder if it is possible to download the db132 including data of
> minor allele frequency for each SNP. Thanks in advance for some tips
> how to do it.
>
> Kind regards
>
> Teresita
>
> Teresita Díaz de Ståhl, PhD
>
> _______________________________________________
> Genome maillist - [email protected]<mailto:[email protected]>
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
#bin chrom chromStart chromEnd name score strand refNCBI
refUCSC observed molType class valid avHet avHetSE func locType
weight exceptions submitterCount submitters alleleFreqCount alleles
alleleNs alleleFreqs bitfields
836 chr13 32929386 32929387 rs169547 0 -
T T A/C/G/T genomic single
by-cluster,by-frequency,by-hapmap,by-1000genomes 0.041813
0.138414 missense exact 1 SingleClassQuadAllelic 26
1000GENOMES,ABI,AFFY,BCM-HGSC-SUB,BCMHGSC_JDW,BGI,BIC_BRODY,BUSHMAN,COMPLETE_GENOMICS,CSHL-HAPMAP,EGP_SNPS,ENSEMBL,GMI,HGSV,HUMANGENOME_JCVI,ILLUMINA,ILLUMINA-UK,KWOK,OSTRANDER,PERLEGEN,SC_JCM,SC_SNP,SEATTLESEQ,SNP500CANCER,SSAHASNP,WUGSC_SSAHASNP,
3 G,A,C, 3230.000000,112.000000,11.000000,
0.963316,0.033403,0.003281,
clinically-assoc,maf-5-some-pop,submitted-by-lsdb,genotype-conflict,rs-cluster-nonoverlapping-alleles
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
