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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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.
Jim
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