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When running the capacitor with BAM input files, I get the following error:

What is going wrong?

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  1. The error is not very self-explanatory, but it comes from the 3rd party SAMtools library we are using. What SAMtools wants to say tell us with that error is that the BAM file has to be sorted for the (necessary) indexing. To sort your bam file, use the command:

    samtools sort aln.bam aln.sorted