Question: Haplotype data for particular populations and a particular gene
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gravatar for genogeno
2.7 years ago by
genogeno0
genogeno0 wrote:

Hi everyone,

I need to get haplotype data for HapMap or 1000 Genomes for CEU, MKK, TSI, CHB and JPT for ± 1 Mb at LCT gene. I'm quite new in the area. Actually I don't know the meaning of "± 1 Mb". From which sites and how do I get the data? Do I need a program?

Thanks!

haplotype • 747 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by genogeno0

As far as I understand, LCT gene is on Chromosome 2. That's why I used following code:

wget -r --reject="index.html*" http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

Now I have a vcf file. I'm not sure what to do with this vcf file.

ADD REPLYlink written 2.7 years ago by genogeno0

Hi, I also obtained a vcf file from Data Slicer ( http://grch37.ensembl.org/Homo_sapiens/Tools/DataSlicer ). I chosed populations and wrote 2:135,787,840-135,837,200 for region lookup. What does this file contain? How can I see the file content? What else do I have to do to get haplotypes? I will try to cluster and visualize haplotypes accorgind to populations. If you can guide me, I am very happy.

ADD REPLYlink written 2.7 years ago by genogeno0
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