Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
TASK:
Write a SHORT vignette (succinct as possible) for the User's Guide describing accessing 1000 genomes file from AWS
Before you get started, spend an hour reading up on the 1000 genomes project, what it is, and so on.
Also, before you get started, see this post on IGV groups:
https://groups.google.com/forum/#!topic/igv-help/Z6vF2n8nzSc[1-25]
Hi everyone,
I would like to compare my own bam file with data from the 1000 Genomes list (I usually pull the last one up through "File -> Load from Server").
I succeeded in writing a batch script that shows my own bam file and saves a snapshot, but how can I add the track from the 1000 Genomes data to this?
Thanks for any help with this!
Best,
~Lina
Hi,
If you know the URL to the file, either ftp or http, you can use "Load from URL..." and paste it in, or the batch load command. For example,
the same data can be loaded from the "cloud" with this URL
In general I recommend use of the cloud URLs, performance will be much better. Unfortunately browsing the cloud dataset is not easy without a tool, however it usually works to first find the data browsing the ftp site at ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/, the replacing the first part of the URL with the cloud eqiuvalent, i.e. replace
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp
with
http://1000genomes.s3.amazonaws.com
For VCF files I recommend just downloading them, they aren't so huge and performance is better. If you want to load them remotely the cloud URLs are your only option (other than downloading the file) as ftp is not supported for tabix indexed files.
Jim
- show quoted text -
On Thursday, August 2, 2012 5:54:24 PM UTC-4, Lina Faller wrote:
Hi everyone,
I would like to compare my own bam file with data from the 1000 Genomes list (I usually pull the last one up through "File -> Load from Server").
I succeeded in writing a batch script that shows my own bam file and saves a snapshot, but how can I add the track from the 1000 Genomes data to this?
Thanks for any help with this!
Best,
~Lina
Attachments
Issue Links
- relates to
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BUG-622 File format issues
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- Closed
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Activity
What happens if you open from url?
Seems like that should work ???
Nope - it does not - I keep getting an error about trying to find chromosomes (from the downloaded file). Could be a VCF issue? Assigning to Hiral to check...
Check if the header is missing the chromosome names
$ samtools view -H URL
I just opened http://1000genomes.s3.amazonaws.com/release/20110521/ALL.chr11.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz and it worked fine.
Btw, http://1000genomes.s3.amazonaws.com/release/20110521/ALL.chr11.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz is a tabix indexed file. So you will need to download corresponding tabix file as well.
I tested using both the .bam file directly from URL:
and the .vcf file directly from URL:
As was commented by Hiral, the .vcf file requires it's accompanying .tbi file. I ended up downloading the .vcf file and the .tbi file as follows and the file worked in IGB:
- Open a new tab/window on browser and in the web address field input the following links and hit enter.
- The files should immediately begin downloading.
- The .vcf file is 7.24GB and the .tbi file is 130KB in size so be prepared timewise.
OR just click on the above links to download both files.
The bam files work just fine but you HAVE to pull down the bai as well (as always).
The vcf file is giving me trouble - still working on it...