Finding CEU / NA12891 data on 1000 genome project

Question

[jnowacki]

Why is it so hard to find CEU / NA12891 on 1000 Genomes:

If I do a site search:

http://www.internationalgenome.org/search/?q=NA12891

Nothing comes up. If I do a browse via the data portal filter CEU samples here:

http://www.internationalgenome.org/data-portal/sample

183 CEU samples show up but no NA12891

Yet clearly the data exists:

http://www.internationalgenome.org/data-portal/sample/NA12891

Why is it so hard to find? I found this thread describing a goal of excluding "all samples who were at least 2nd degree relations of other samples in the set, this was to avoid double counting alleles when calculating allele frequencies." So I guess it doesn't fit with the primary goal of 1,000 genomes but is there a way to find ALL data that's stored at that repository?

A: Why the CEU trio's parents NA12891 and NA12892 are not in 1000 Genomes phase 3

[Emily]

I don't understand what you mean that it's hard to find. You found it by doing a search, so what's hard to find about it?

Answer 1

[Pierre Lindenbaum]

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree" | grep NA12891

ftp/data_collections/illumina_platinum_pedigree/data/CEU/NA12891/alignment  directory   263 Wed Oct 14 19:36:48 2015
ftp/data_collections/illumina_platinum_pedigree/data/CEU/NA12891/alignment/NA12891.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram.crai file    2841310 Wed Oct 14 08:04:36 2015    a91d56f2e2705b33b0da27ba845707db
ftp/data_collections/illumina_platinum_pedigree/data/CEU/NA12891/alignment/NA12891.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.bam.bas   file    631 Fri Aug 28 15:03:39 2015    37ca80626ca2b9838d689884c0dd878a
ftp/data_collections/illumina_platinum_pedigree/data/CEU/NA12891/alignment/NA12891.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cramfile  39317315882 Wed Oct 14 06:52:46 2015    c98e5b10b9bc16c2f012adf09d16d72a
ftp/data_collections/1000_genomes_project/data/CEU/NA12891/exome_alignment  directory   215 Tue Nov 10 11:12:10 2015
ftp/data_collections/1000_genomes_project/data/CEU/NA12891/exome_alignment/NA12891.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram  file    6932970668  Mon Nov  9 07:07:52 2015    505e4a4918970e5941d8044f074dca2c
ftp/data_collections/1000_genomes_project/data/CEU/NA12891/exome_alignment/NA12891.alt_bwamem_GRCh38DH.20150826.CEU.exome.bam.bas   file    610 Sun Sep 13 14:13:49 2015    88bf398f9d92c17ddae54bf3c652e335
ftp/data_collections/1000_genomes_project/data/CEU/NA12891/exome_alignment/NA12891.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram.crai file    487506  Mon Nov  9 07:07:53 2015    c2f3a4d325f3d4870125da798bd16095
ftp/data_collections/1000_genomes_project/working/20160216_pgenome_fastas/NA12891_pgenome_hg19.tgz  file    1769735888  Tue Feb  9 01:19:41 2016    046b919cbd8d98a431e23ea6be831050
ftp/phase1/technical/other_exome_alignments/NA12891/exome_alignment directory   212 Tue Dec 13 12:53:15 2011
ftp/phase1/technical/other_exome_alignments/NA12891/exome_alignment/NA12891.mapped.ILLUMINA.BWA.CEU.exome.20110521.bam.bas  file    543 Tue Jul 12 13:36:09 2011    21a42f7542a0e2eda7905208e31d3105
ftp/phase1/technical/other_exome_alignments/NA12891/exome_alignment/NA12891.mapped.ILLUMINA.BWA.CEU.exome.20110521.bam.bai  file    7847928 Tue Jul 12 09:09:52 2011    12c72a2f258611a1d76e5e00705d1763
(...)

[jnowacki]

That is awesome. Thank you!

[Pierre Lindenbaum]

if it answered your question, please check the green mark on the left to close, thanks.