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I have aligned two whole genomes of the same species in Mauve using progressiveMauve. One of the genomes is 2 megabases longer than the other so I know it must contain some insertions. Looking at the alignment in the Mauve GUI, it seems that insertions are small and scattered throughout the genome. I have exported the SNPs from the GUI. Is there a similar option for indels? I have also inspected the Mauve file written after the alignment. It contains the two original sequences in FASTA format but I noticed in contains gaps denoted by a dash (-). Would it be possible to create a VCF from that file?

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