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Old 11-08-2010, 12:59 PM   #1
Alessandra
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Location: Philadelphia

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Question tabix and 1000 genomes data

Hi,

I am trying to access the latest release of the 1000 genomes data to check a few snps. In the README file they say:
"Each file has a tabix index associated with it allowing subsections to be downloaded using the tabix program... like this:
tabix
ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz 1:233411980-245804116"

I did that and I got a .tbi file. How do I open it or access it to look at the variants? I could not find any documentation explaining that.

Thank you for your help!

Alessandra
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Old 12-11-2010, 08:52 PM   #2
johnadam33
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Have u figured it out? I am in the same boat. Can u tell me how you did it? Thanks. John.
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Old 01-05-2011, 02:07 AM   #3
laura
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the tbi file it downloaded was the index file it uses to find the variants

It should of also streamed the section vcf file to STDOUT and you will need to capture this in a file

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz 1:233411980-245804116 > myfile.vcf

should give you a vcf file

Its best to use the -h option from tabix as this gives you the header which is important for interpreting the file correctly
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Old 02-04-2011, 02:39 AM   #4
AndreaL
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Hi,

I've red that someone had some problem with tabix. I have Windows 7 and I dowloaded tabix (tabix-0.2.3.tar.bz2) but I don't know how to install it. I use Samtools and I have no problems but with Tabix I'm in trouble. Could some one give me an help on how install it and make it work?

Thanks

Andrea
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Old 03-03-2011, 02:49 AM   #5
mimi_lupton
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Question

Hi,
I have a quick question about using tabix on the 1000 genomes data. I have used it to download some regions I am interested in. But I haven't got the header so I can't see the sample order. I thought there must be a way to ask tabix for the header, I tried what Laura mentions, but it says -h is not an option? Am I missing something?

Thanks


Quote:
Originally Posted by laura View Post
the tbi file it downloaded was the index file it uses to find the variants

It should of also streamed the section vcf file to STDOUT and you will need to capture this in a file

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz 1:233411980-245804116 > myfile.vcf

should give you a vcf file

Its best to use the -h option from tabix as this gives you the header which is important for interpreting the file correctly
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Old 03-03-2011, 03:19 AM   #6
laura
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what version of tabix are you using -h only appeared in version 0.2.3
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Old 03-03-2011, 03:24 AM   #7
mimi_lupton
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Hi Laura,
Thanks very much for you quick reply, I have version 0.2.1 so I will download a newer one and try that.
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Old 09-04-2013, 10:34 PM   #8
zhanxw
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Default My compiled version of tabix

You can download my compiled version of tabix here:

http://zhanxw.com/blog/2013/09/windo...rmatics-tools/

Quote:
Originally Posted by Alessandra View Post
Hi,

I am trying to access the latest release of the 1000 genomes data to check a few snps. In the README file they say:
"Each file has a tabix index associated with it allowing subsections to be downloaded using the tabix program... like this:
tabix
ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz 1:233411980-245804116"

I did that and I got a .tbi file. How do I open it or access it to look at the variants? I could not find any documentation explaining that.

Thank you for your help!

Alessandra
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Old 09-05-2013, 12:13 AM   #9
rhinoceros
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Sometimes I feel like some things in bioinfo have been made rather difficult on purpose. The available 1,000 genomes data is a perfect example of this. There's some truth to this rant..

Sorry for the off-topic..
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