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After a struggle to get samtools successfully installed and working on my windows machine, I'm now having trouble (I think) indexing a bam file. I'm using cygwin to use samtools. I'm planning on visualizing a metagenomic sequence for SNP screening in IGV but the bam file format isn't supported. A message pops up saying that the bam file needs to be indexed. In samtools I'm using ./samtools sort <file.bam> <file.sorted> and a sorted file is successfully made. However when I go to index the file using ./samtools index file.sorted.bam a 24kb file is made. Is there something I'm doing wrong here? Thank you all for your help so far.
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IGV supports .bam files. I look at indexed .bam files all the time on IGV. It woud be rather useless software if it didn't handle .bams. 24 kb sounds about right for the index. Make the index, then try to load the .bam into IGV. -
IGV will also index them for you if you do not have one.Comment
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When I try to load a .bam file it tells me it needs to be indexed. Do I have to load both the .bam and the index simultaneously?Comment
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No, just load the .bam. IGV will lok for a .bam.bai with the same name in the directory with the .bam, and when it finds it, it will work.Comment
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Thank you for your help guys, I got it to work.Comment
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Hi,
I'd like to make a slight correction for the benefit of future googlers. IGV will not create an index for a BAM file, although we might add this in the future. Use samtools or Picard to create such an index. It will index a SAM file for you, that is an IGV specific index created before the BAM index spec and implementation were finished, i.e. a long time ago. We keep it for backward compatibility, but it is not the same index as the BAM file index.
JimComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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