Question: How to get IDs of family trios in 1000 genomes project?
0
gravatar for GabrielMontenegro
2.5 years ago by
United Kingdom
GabrielMontenegro540 wrote:

I know that several populations from the 1000 genomes project have trio data on them, but I just couldn't find it anywhere on the site.

This is the VCF files that I am currently using: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/vcf_with_sample_level_annotation/

I found this post here, but it is not updated: 1000 Genomes: Where To Get Samples Description Some populations that are available now are not listed there.

Thank you.

genome • 1.6k views
ADD COMMENTlink modified 2.5 years ago by Petr Ponomarenko2.6k • written 2.5 years ago by GabrielMontenegro540
2
gravatar for Petr Ponomarenko
2.5 years ago by
United States / Los Angeles / ALAPY.com
Petr Ponomarenko2.6k wrote:

Pierre answer is perfect, but this file ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v2.20130502.ALL.ped might be easier for understanding. When we only want trios then we usually use main set ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ together with ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/related_samples_vcf/ and ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/related_samples_vcf/related_samples_panel.20140910.ALL.panel and you can simply grep for these individuals in the main ped file

ADD COMMENTlink written 2.5 years ago by Petr Ponomarenko2.6k

Thanks, the ped file is what I was looking for. Would you mind explaining what the current tree file is showing?

ADD REPLYlink written 2.5 years ago by GabrielMontenegro540

See here for an explanation of the ped (pedigree) file.

ADD REPLYlink written 2.5 years ago by andrew.j.skelton735.8k

That's the ped file. I meant the current tree file.

ADD REPLYlink written 2.5 years ago by GabrielMontenegro540
1
gravatar for Pierre Lindenbaum
2.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:
 wget -O - "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree" | grep -i trio
ADD COMMENTlink written 2.5 years ago by Pierre Lindenbaum123k

Hi Pierre. Thanks for the quick reply. Could you help me understand this data? I don't know exactly what I am looking at? I am trying to find the specific IDs of fathers,mothers and childs for all the trios in 1KG. Also, I did a quick grep for PEL, the Peruvian population that I know was included in the last phase and there's no information on them.

ADD REPLYlink written 2.5 years ago by GabrielMontenegro540
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