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,

ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00111/alignment/HG00111.chrom11.ILLUMINA.bwa.GBR.low_coverage.20111114.bam

the same data can be loaded from the "cloud" with this URL

http://1000genomes.s3.amazonaws.com/data/HG00111/alignment/HG00111.chrom11.ILLUMINA.bwa.GBR.low_coverage.20111114.bam

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.

http://1000genomes.s3.amazonaws.com/release/20110521/ALL.chr11.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz

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