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Old 06-02-2011, 05:42 AM   #1
jorjial
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Default 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 07:23 AM.
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Old 06-03-2011, 12:38 AM   #2
jorjial
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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. "
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Old 06-03-2011, 04:32 AM   #3
Yilong Li
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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.
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Old 06-06-2011, 03:16 AM   #4
jorjial
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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
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1000 genomes project, alignment, exome, ngs

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