Extracting (Slicing) a BAM file

[ashkot]

Hi there, i was wondering if someone could help with this. As there are several larger .bam files i wanted to slice out only data that belongs to say chromosome.

I found the following command on 1kGenomes site but it does not work.

samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...e.20101123.bam 17:7512445-7513455

Can someone please help me the correct command syntax, i want to download .bam or .vcf files for full chromosomes such as 1,2 or 12 etc without specifying the genomic coordinates.

Thanks in advance.

Ashwin

[mhayes]

The syntax looks okay. How were the chromosomes labeled in the reference fasta file? Is it "chr17" or just "17"?

Also, is samtools capable of reading a BAM file remotely? Should you download it first?

What errors are being returned by the program when you try to execute it?

[ashkot]

I was trying to follow as show on this site.

http://www.1000genomes.org/faq/how-do-i-get-sub-section-vcf-file

The program does not generate any errors as such, just the output file shows junk.

Any ideas?

[hanshart]

hi,

I just wanted to try it out but it seems that most of the HG... files were changed today. So I looked for another folder containing any BAM-files. Executing

samtools view ftp://ftp.1000genomes.ebi.ac.uk/vol1...d.20100311.bam 1:470260-471000 > test.sam

everything worked correctly (also "view -h"). So your command should be ok but the data seems to be corrupt (?)

cheers

[ashkot]

when i was looking at the screen, at the output, it showed a lot of error verbiage. so i wasnt sure altogether what was going on. I will give your suggested command a try and update this forum as well.