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  • problem indexing a bam file

    I need to slice my bam file to look at the reads in a small region using IGV. I used samtools version 0.1.18 to do that but I am having problem indexing the .bam file, here is what I did

    samtools view myfile.bam chr2:20,100,000-20,200,000 > outfile.bam
    samtools index outfile.bam

    I am getting the following error message

    [bam_header_read] EOF marker is absent. The input is probably truncated.
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    Segmentation fault (core dumped)

    Any ideas?

  • #2
    Originally posted by kjaja View Post
    I need to slice my bam file to look at the reads in a small region using IGV. I used samtools version 0.1.18 to do that but I am having problem indexing the .bam file, here is what I did

    samtools view myfile.bam chr2:20,100,000-20,200,000 > outfile.bam
    samtools index outfile.bam

    I am getting the following error message

    [bam_header_read] EOF marker is absent. The input is probably truncated.
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    Segmentation fault (core dumped)

    Any ideas?
    You didn't make a .bam file. You made a .sam file. Look at it, it's plain txt.

    Code:
    samtools view [B]-b[/B] myfile.bam chr2:20,100,000-20,200,000 > outfile.bam
    samtools index outfile.bam
    You have to add in the -b option to make the output .bam. Default behavior for samtools view is to make a .sam file.

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