Pysam: Is there a way to check if there are inserts when looking at read overalps.
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2.6 years ago

From a bam file I have a set of reads. For each read I am only interested in a particular regions, baring there is a continuous sub-sequence (i.e no gaps) and that their are no inserts.

With pysam I have been able to check for overlap in the reads using: .get_overlap(start_pos, end_pos) . Where I hit a road block is checking if an insert or deletion is within that region. Are there any built in pysam functions that would tell me this?

Thanks!

alignment pysam • 1.0k views
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I think you'll have to check the cigar

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