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  • Extracting (Slicing) a BAM file

    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

  • #2
    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?

    Comment


    • #3
      I was trying to follow as show on this site.

      1000genomes.org is your first and best source for all of the information you’re looking for. From general topics to more of what you would expect to find here, 1000genomes.org has it all. We hope you find what you are searching for!


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

      Any ideas?

      Comment


      • #4
        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

        Comment


        • #5
          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.

          Comment

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