1000 Genomes Data Download/Tabix

[strongside24]

Hi,

I am trying to download 1000 Genomes data using tabix. But I am unsure of how to do this. I searched through previous threads and could not find a step by step tutorial of how to do this.

I have tabix downloaded on PuTTY, but am not sure where to go from here. Step by step instructions or a tutorial would be much appreciated.

Thanks in advance!

[laura]

Have you tried our example command lines from the faq

http://www.1000genomes.org/faq/how-do-i-get-sub-section-vcf-file

[strongside24]

Yes, I tried copy pasting that command line but it does not work and says that is not a function. Please help! Thanks!

[laura]

Can you post your full command line and any error messages you see so we can help

[strongside24]

i posted :

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...lease/20100804 ALL.2of4intersection.20100804.genotypes.vcf.gz 2:39967768-39967768

and this came up:

[kftp_connect_file] 550 Could not get file size.
[main] fail to open the data file.


thanks!

[laura]

Apologies this is due to a typo in the example, there is a space between the ftp directory and the filename where there should be a /

[strongside24]

i tried replacing the space witha / and i got the same error message.

i posted this:

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz 2:39967768-39967768

and got the same results.

help please! thank you!

[strongside24]

wait nevermind. got it to work. thank you so much! will let you know if i have any more questions!!

[strongside24]

i finished downloading the data i need via tabix, but now i am unsure of how to use it. how do you convert it into genotypes that can be useable in pli for an ld analysis?

thanks!

[GenoMax]

how do you convert it into genotypes that can be useable in pli for an ld analysis?

thanks!

Perhaps like this: http://www.1000genomes.org/faq/can-i...linkped-format

[strongside24]

i tried that command, and it said this:

"Can't open perl script 'vcf_to_ped_converter.pl': No such file or directory"

What is this script, and how do I get it?

Much appreciated!

[GenoMax]

i tried that command, and it said this:

"Can't open perl script 'vcf_to_ped_converter.pl': No such file or directory"

What is this script, and how do I get it?

Much appreciated!

It seems to be available here: ftp://ftp.1000genomes.ebi.ac.uk/vol1...r/version_1.1/

[strongside24]

Actually scratch that.

I'm using the online VCF to PED Converter here: http://browser.1000genomes.org/Homo_...Data/Haploview

But when I download everything, it does not pull all the variants. It leaves out the introns. For example, I tried pulling mapk1. I entered the region I found through the browser and resulted 1619, not the 6777. I'm assuming the introns are left out. Is there a way to do this so all variants are pulled/downloaded?

Thanks!!

[strongside24]

Also, is the online converter the same as the VCF to PED converter Genomax referenced above? And is there a way to pull introns from this converter as well? Thanks!

[GenoMax]

Also, is the online converter the same as the VCF to PED converter Genomax referenced above? Thanks!

One would hope so since there appears to be only one version available for download.

Perhaps Laura can confirm by tomorrow.