Entering edit mode
6.0 years ago
2012secondseason
▴
40
Hi. I'am so curious about Padded Alignment. In situation like this,
REF: CACGATCA**GACCGATACGTCCGA
READ1: CGATCAGAGACCGATA
READ2: ATCA*AGACCGATAC
READ3: GATCA**GACCG
The padded CIGAR are different:
READ1: 6M2I8M
READ2: 4M1P1I9M
READ3: 5M2P5M
In what cases, READ2 is not to just 4M1I9M but to 4M1P1I9M ? Thanks.