Download bam region from 1000 genome project

[marco12345]

Hi,

I am trying to download only one (or more) region from a bam file from the 1000 Genome Project without having to download the whole file.
The way the 1000GP website suggests seems not to work for me, and I can't pinpoint the problem. Could you please help me?

I am working on a cluster using Linux.
Here's the command I sent:
samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...e.20120522.bam 17:41243452-41277500 > HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.chr17reg1.bam

The resulting file is an empty bam with no header.

Thanks!

[GenoMax]

There must be some sort of restriction (firewall?) for using ftp on your cluster node. I did get a output file using your command. Output is in SAM format BTW, using your command.

[lre1234]

I can also get the command that you have to work fine. But I have been trying to get this to work with using the '-L MyRegions.bed' samtools command to get multiple regions from a bed file, but it doesn't seem to work. Is that not allowed with using the ftp file?

[lh3]

It should work, but will be very slow.