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Friday, May 16, 2014

Create Index for BAM File

Sometimes databases or contributors share .BAM files, but fail to provide the associated BAM index file (the .BAI file). The BAM index file, usually named filename.bam.bai, is needed to visualize the reads in IGV as well as several other applications. Samtools can easily generate an index file for your sequence bam file. The below code is an example of how to do so for a bam file called filename.bam.

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