Problems Accessing 1000G Data

I am just copy+pasting from the 1000g instructions here:
http://www.1000genomes.org/faq/how-do-i-get-sub-section-bam-file

samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17:7512445-7513455

But I can't get it to work:

~/samtools-0.1.12a/samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17:7512445-7513455
[kftp_connect_file] 550 Could not get file size.
[main_samview] fail to open "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam" for reading.

Any ideas?

bam samtools genome

• 3,488 views • link

updated 10.3 years ago by Biostar

• written 14.5 years ago by Ahdf-Lell-Kocks •

1 answer

1000 Genomes regenerated alignments for some of their datasets I seem to recall, therefore they have different names. If you go to the FTP directory in a browser, it is still there, but the file is not.

I think you want this file :

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20111114.bam

• 3 views • link

written 14.5 years ago by User 59

Indeed this file no longer exists

We will fix our documentation but in the meantime you can always use the ftp search to find another bam file

http://www.1000genomes.org/ftpsearch

• 0 views • link

written 14.5 years ago by Laura

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