gencore seems to have wrongly modified my SAM alignment record #47
Description
Hi,
Gencore seems to have wrongly modified my SAM alignment record.
I have SAM record as below:
NS500830:1150:HWNN2AFX3:2:11202:24875:15467:GGT_GGC 161 chr7 55268915 60 71M chrUn_gl000220 132375 0 ACTCCAACTTCTACCGTGCCCTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTC /AEEEAEEEEAEEEEEEEEEEEAEEEAAEEEEEEEEEEEEEEEEE/AEEEAEEEEEEEEEEAEEEE/EEE< NM:i:0 MD:Z:71 MC:Z:71M AS:i:71 XS:i:19 RG:Z:BT2302040049LNCBC NS500830:1150:HWNN2AFX3:2:11202:24875:15467:GGT_GGC 81 chrUn_gl000220 132375 57 71M chr7 55268915 0 TCTCTCTCTCTCTCTCTCTCTGCCTCTCTCACTGTGTCTGTCTTCTGTCTTATTCTCTTTCTCTCTCTGTC EEEEEEAEEEEEEEEEEEEEEEAEEEEEEEEAEAEE/EEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE NM:i:0 MD:Z:71 MC:Z:71M AS:i:71 XS:i:52 RG:Z:BT2302040049LNCBC
but, after gencore remove duplicate reads using s=2, I got
NS500830:1150:HWNN2AFX3:2:11202:24875:15467:GGT_GGC 161 chr7 55268915 60 71M chrUn_gl000220 132375 0 ACTCCAACTTCTACCGTGCCCTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTC EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE NM:i:0 MD:Z:71 MC:Z:71M AS:i:71 XS:i:19 RG:Z:BT2302040049LNCBC NS500830:1150:HWNN2AFX3:2:11202:24875:15467:GGT_GGC 145 chrUn_gl000220 132375 25 71M chr7 55268915 0 TCTCTCTCTCTCTCTCTCTCTGCCTCTCTCACTGTGTCTGTCTTCTGTCTTATTCTCTTTCTCTCTCTGTC EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE NM:i:1 MD:Z:7C63 MC:Z:69M2S AS:i:66 XS:i:57 RG:Z:BT2302040049LNCBC XA:Z:chrY,-10024049,71M,4;
why 81 convert to 145?
Thx