How to get IDs of family trios in 1000 genomes project?

Question

[GabrielMontenegro]

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.

Answer 1

[Petr Ponomarenko]

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

[GabrielMontenegro]

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

[andrew.j.skelton73]

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

[GabrielMontenegro]

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

Answer 2

[Pierre Lindenbaum]

 wget -O - "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree" | grep -i trio

[GabrielMontenegro]

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.