Problems Accessing 1000G Data

Question

[Ahdf-Lell-Kocks]

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?

Answer 1

[User 59]

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

[Laura]

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