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Download Specific Individuals From Dbsnps?

I'm trying to get the variation data from dbSNP for a specific Coriell sample (NA07029) and it is surprisingly difficult. I can find the sample individual report here but there are no information about the variations found in this individuals. I tried downloading the whole dbSNP in vcf hoping to find sample information that I could filter on but there aren't any.

I feel like I'm missing something obvious here

human variation
• 2,768 views • link
updated by Ram Ram • written by tcezard • tcezard

2 answers

I found those data in the hapmap database:

$ curl -s "http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/latest/forward/non-redundant/genotypes_chr1_CEU_r27_nr.b36_fwd.txt.gz" |\
gunzip -c |\
cut -d ' ' -f 1-11,25 |\
verticalize -d ' ' 

>>> 2
$1 rs#       rs10399749
$2 alleles   C/T
$3 chrom     chr1
$4 pos       45162
$5 strand    +
$6 assembly# ncbi_b36
$7 center    perlegen
$8 protLSID  urn:lsid:perlegen.hapmap.org:Protocol:Genotyping_1.0.0:2
$9 assayLSID urn:lsid:perlegen.hapmap.org:Assay:25761.5318498:1
$10 panelLSID urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1
$11 QCcode    QC+
$12 NA07029   CC
<<< 2

>>> 3
$1 rs#       rs4030303
$2 alleles   A/G
$3 chrom     chr1
$4 pos       72434
$5 strand    +
$6 assembly# ncbi_b36
$7 center    sanger
$8 protLSID  urn:lsid:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1
$9 assayLSID urn:lsid:sanger.hapmap.org:Assay:4319326:1
$10 panelLSID urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1
$11 QCcode    QC+
$12 NA07029   GG
<<< 3
• 2 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre Exactly what I was looking for

• 0 views • link
written by tcezard • tcezard

This sample is part of the hapmap project. Try the ftp repository here

Genotypes are publicly available.

• 0 views • link
written by ff.cc.cc ff.cc.cc

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