bam files of exomes from 1000 genomes

jorjial · 06-02-2011, 06:42 AM

Hi everybody,
I'm working with some exome sequencing data. I'd like to compare my results with data from 1000 genomes project. I have not found any public list of alignment files in bam format. But, if you browse the samples data directories in the FTP server, you can find some alignment files in bam format. For example, in this directory ftp://ftp.1000genomes.ebi.ac.uk/vol1...ome_alignment/. Does anyone know if these files are the definitive ones? Or some of them are partial alignments and they are going to complete them?
Thanks a lot!
Jrg

jorjial · 06-03-2011, 01:38 AM

This is the answer from the 1000 genomes project:
"The exome BAMs you found on the ftp site are a part of the Phase I data. It is incomplete. Some samples don't have exome BAMs yet; some samples have BAMs but the BAM may be updated due to additional sequences are added in the future. "

Yilong Li · 06-03-2011, 05:32 AM

Check ftp://ftp.1000genomes.ebi.ac.uk/vol1...lignment.index. There should be all alignments available from 1000G repository atm and some annotation like the population of origin. And also the locations of the files where you can deduce if they are exome sequencing data or not.

jorjial · 06-06-2011, 04:16 AM

Hi Yilong,
Thanks for your answer. There are not exome alignment in this file. But, if you browse the FTP server, you can find some exome alignment in the corresponding sample folder. The problem is that some of them are partial alignment, but you can't differentiate them.
Jrg

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Convert 1000-Genomes-proje BAM to FASTA (aligned to reference, grouped by chromosome)	ce.log	Bioinformatics	17	01-14-2014 12:35 AM
1000 Genomes VCF Files	ashkot	Bioinformatics	8	02-25-2013 03:12 PM
confused by all the 1000 Genomes fastq files	efoss	Bioinformatics	3	10-11-2011 07:43 AM
using BWA to align SOLiD fastq files from 1000 Genomes	tgenahmet	Bioinformatics	1	10-15-2009 06:19 PM
.bam alignment format from 1000 Genomes Project	CellsDividing	Bioinformatics	2	02-06-2009 09:21 AM

06-02-2011, 06:42 AM	#1
jorjial Junior Member Location: Valencia Join Date: Mar 2010 Posts: 7	bam files of exomes from 1000 genomes Hi everybody, I'm working with some exome sequencing data. I'd like to compare my results with data from 1000 genomes project. I have not found any public list of alignment files in bam format. But, if you browse the samples data directories in the FTP server, you can find some alignment files in bam format. For example, in this directory ftp://ftp.1000genomes.ebi.ac.uk/vol1...ome_alignment/. Does anyone know if these files are the definitive ones? Or some of them are partial alignments and they are going to complete them? Thanks a lot! Jrg Last edited by jorjial; 06-02-2011 at 08:23 AM.

06-03-2011, 01:38 AM	#2
jorjial Junior Member Location: Valencia Join Date: Mar 2010 Posts: 7	This is the answer from the 1000 genomes project: "The exome BAMs you found on the ftp site are a part of the Phase I data. It is incomplete. Some samples don't have exome BAMs yet; some samples have BAMs but the BAM may be updated due to additional sequences are added in the future. "

06-03-2011, 05:32 AM	#3
Yilong Li Member Location: WTSI Join Date: Dec 2010 Posts: 41	Check ftp://ftp.1000genomes.ebi.ac.uk/vol1...lignment.index. There should be all alignments available from 1000G repository atm and some annotation like the population of origin. And also the locations of the files where you can deduce if they are exome sequencing data or not.

06-06-2011, 04:16 AM	#4
jorjial Junior Member Location: Valencia Join Date: Mar 2010 Posts: 7	Hi Yilong, Thanks for your answer. There are not exome alignment in this file. But, if you browse the FTP server, you can find some exome alignment in the corresponding sample folder. The problem is that some of them are partial alignment, but you can't differentiate them. Jrg