Entering edit mode
5.1 years ago
ahmed.kidwai
•
0
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!
I think you'll have to check the cigar