[g781]

Hi everyone,

I have the same problem as below:

SEA055486C:139:C06FAACXX:6:2207:3530:3130       83      chrVII  675196  60      59M42S  =       675159  -96     TTGTTCGTGATGCTTCCGAAATTCCCGAAGGTTGCGTATTGCAATCTGTTAACCCAGAATCAGCCAGAACAAGAAGGACAAAGTGATCAAGACATAGGGAA  C>59<DCCDCDDDDB?CCCCCAB9,.HHHJJJIGIJIJIIJIGGE@FGIGHDEGEHFHGEGCG<EHDHHIIJIIHEHDGHHHGGGIGGFHHHFFDDFDCC@   NM:i:1  AS:i:54 XS:i:0  XP:Z:chrXVI,-908080,52S49M,60,0;
[COLOR="Red"]SEA055486C:139:C06FAACXX:6:2207:3530:3130       83      chrXVI  908080  60      52S49M  chrVII  675159  0       TTGTTCGTGATGCTTCCGAAATTCCCGAAGGTTGCGTATTGCAATCTGTTAACCCAGAATCAGCCAGAACAAGAAGGACAAAGTGATCAAGACATAGGGAA  C>59<DCCDCDDDDB?CCCCCAB9,.HHHJJJIGIJIJIIJIGGE@FGIGHDEGEHFHGEGCG<EHDHHIIJIIHEHDGHHHGGGIGGFHHHFFDDFDCC@   NM:i:0  AS:i:49 XS:i:0  XP:Z:chrVII,-675196,59M42S,60,1;[/COLOR]
SEA055486C:139:C06FAACXX:6:2207:3530:3130       163     chrVII  675159  60      96M5S   =       675196  96      ATTGTCTCGTTGATCAAGGCCATCGACGAAGTCACTGTTGTTCGTGATGCTTCCGAAATTCCAGAAGGTTGCGTATTGCAATCTGTTAACCCAGAATCAGC  B@@DBDDFHBFHDGIGGIIGHGGDCGIGEHH?BGHICGGHIIGI?FEGGEFA@FGGGEHHHGHEDEFF>AE@BB?BDDDDDDDD@DDCE>CBBDBDA@CCD   NM:i:0  AS:i:96 XS:i:0

The read marked in red was aligned on different chromosomes. I have no idea what's happened to this case. Is it caused by the split algorithm?

Thanks.

[shuoguo]

I had the same error when I use an older version of picard (1.45). After downloading the newest picard (1.129) I no longer have the issue. Even without the -M option while mapping with bwa mem