Extract number of INDELs of a specific position for bam file or IGV

I'm working with Nanopore data that naturally has a lot of INDELs. Is there a way to get all the deletions/insertions from a specific position in the genome for all reads, as shown in IGV? (I would like to get it for many positions)

Thanks

alignment ngs igv indels nanopore

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written 5.9 years ago by igit_b •

Take a look at igvtools included in IGV or bamcount (LINK).

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written 5.9 years ago by GenoMax

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