tabix and 1000 genomes data

Alessandra · 11-08-2010, 12:59 PM

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

johnadam33 · 12-11-2010, 08:52 PM

Have u figured it out? I am in the same boat. Can u tell me how you did it? Thanks. John.

laura · 01-05-2011, 02:07 AM

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

AndreaL · 02-04-2011, 02:39 AM

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

mimi_lupton · 03-03-2011, 02:49 AM

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

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

laura · 03-03-2011, 03:19 AM

what version of tabix are you using -h only appeared in version 0.2.3

mimi_lupton · 03-03-2011, 03:24 AM

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.

zhanxw · 09-04-2013, 10:34 PM

You can download my compiled version of tabix here:

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

Quote:

Originally Posted by Alessandra

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

rhinoceros · 09-05-2013, 12:13 AM

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..

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Interpreting 1000 Genomes data	ashkot	Bioinformatics	5	01-05-2012 12:27 AM
Annotating 1000 Genomes data	ashkot	Bioinformatics	4	12-22-2011 10:53 AM
1000 Genomes Data	RichardRocca	General	1	03-16-2011 12:11 PM
1000 Genomes Data/ Exon targetted	Firebird	Bioinformatics	27	02-17-2011 12:08 PM
need 1000 genomes data for just one gene	michelle.lupton	Bioinformatics	11	08-09-2010 01:00 PM

11-08-2010, 12:59 PM	#1
Alessandra Junior Member Location: Philadelphia Join Date: May 2010 Posts: 2	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

12-11-2010, 08:52 PM	#2
johnadam33 Member Location: Texas Join Date: Oct 2010 Posts: 26	Have u figured it out? I am in the same boat. Can u tell me how you did it? Thanks. John.

01-05-2011, 02:07 AM	#3
laura Senior Member Location: Cambridge UK Join Date: Sep 2008 Posts: 151	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

02-04-2011, 02:39 AM	#4
AndreaL Junior Member Location: Italy Join Date: Feb 2011 Posts: 2	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

03-03-2011, 03:19 AM	#6
laura Senior Member Location: Cambridge UK Join Date: Sep 2008 Posts: 151	what version of tabix are you using -h only appeared in version 0.2.3

03-03-2011, 03:24 AM	#7
mimi_lupton Member Location: Brisbane, Australia Join Date: Oct 2008 Posts: 19	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.

09-05-2013, 12:13 AM	#9
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	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..