Re: [Bio-bwa-help] flag differ between bwa mem & bwa sampe

[Heng Li <lh...@me...>]

The insert size estimate may be different. Please send to bio...@so... in future.

Thanks,

Heng

On Aug 6, 2014, at 9:33 AM, Jia Ding <di...@mp...> wrote:

> Dear Heng Li,
> 
> I am using the most recent bwa version 0.7.10.
> 
> I have paired-end reads of 101bp length.  I tried both mem and sampe. But they gave me different flag!
> 
> e.g.
> ---------------------- with sampe, the flag is 83
> HWI-ST863:323:C3FYHACXX:4:2306:6589:2323    83    3    19767923 60    88M    =    19767826    -185 CATCAGATTACTTGTTACAACTTAAAACAAAACTCAACTCAACTCCACAAGTAAAATGTCATCAAAGTCATAGAGTCTCTCTGTTTCA DEDEEEEEEEEFFDFFFFHHHEHCEIHJJJHFJIIHHJJJIHIGJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJIJJJJJJJJJH XT:A:U    NM:i:0    SM:i:37    AM:i:37    X0:i:1    X1:i:0 XM:i:0    XO:i:0    XG:i:0    MD:Z:88
> 
> 
> -----------------------with mem, the flag is 81
> HWI-ST863:323:C3FYHACXX:4:2306:6589:2323        81      3 19767923        60      88M     =       19767826        -185 CATCAGATTACTTGTTACAACTTAAAACAAAACTCAACTCAACTCCACAAGTAAAATGTCATCAAAGTCATAGAGTCTCTCTGTTTCA DEDEEEEEEEEFFDFFFFHHHEHCEIHJJJHFJIIHHJJJIHIGJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJIJJJJJJJJJH NM:i:0  MD:Z:88 AS:i:88 XS:i:0
> 
> 
> Why the "flag" is different between those two option? It's important for me, as it effect my further analysis.
> 
> Thanks,
> Jia
>