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I recently used pbmm2 to align my reads to the reference genome, when I specified --sort option it is generated a file with extension bam.bai. Afterwards, an index with extension .bam.pbi was generated with pbindex. IGV could not open .bam.pbi, so I tried with bam.bai. The first time I could see the mapping, but I have tried the same steps as the first time and I cannot see the coverage of the reads.

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  • $\begingroup$ What file did you open? Have you tried opening the .bam file? $\endgroup$
    – terdon ♦
    Commented Jun 14 at 9:21

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You should just open the bam file, not one of the index files.

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