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Old 05-05-2011, 02:31 PM   #1
GregRM
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Default NCBI varpipe data from 1000 Genomes Project

I noticed this directory in the 1000 Genomes Project files today, which seems to contain sequence alignment data: ftp://ftp.1000genomes.ebi.ac.uk/vol1...ata/alignment/ . Does anyone know what the NCBI varpipe data is or what "varpipe" refers to? (Also, any idea why it's in the "technical" folder rather than the "data" folder?)
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Old 05-06-2011, 04:36 AM   #2
laura
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Hi Greg

The NCBI Varpipe data is an alternative alignment set being created using the 1000 genomes data.

It is not under data as it isn't included in the official alignment release as described by the alignment index ftp://ftp.1000genomes.ebi.ac.uk/vol1...lignment.index

We are presenting it on the ftp site as this data is being used to support some of our multiple snp calling pipelines and we want users to be able to see as much of the data which goes into our pipelines as possible

If you have any other questions about the 1000 genomes data set you can always email info@1000genomes.org

thanks
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Old 05-08-2011, 07:32 PM   #3
GregRM
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Thanks very much, Laura. I also came across this pdf which seems to provide further details on this approach: http://www.bbmriwiki.nl/raw-attachme...-20100913d.pdf
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