In what cases, does Padded Alignment apply?
Hi. I'am so curious about Padded Alignment. In situation like this,
REF: CACGATCAGACCGATACGTCCGA READ1: CGATCAGAGACCGATA READ2: ATCA*AGACCGATAC READ3: GATCAGACCG The padded CIGAR are different:
READ1: 6M2I8M READ2: 4M1P1I9M READ3: 5M2P5M In what cases, READ2 is not just 4M1I9M but 4M1P1I9M ?
Thanks.
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In what cases, does Padded Alignment apply?
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This is a duplicate of In what cases, does Padded Alignment apply? which was closed for reasons mentioned previously. I'm closing this as well until those issues are rectified.