problem indexing a bam file

[kjaja]

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?

[swbarnes2]

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.

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.