pezmaster31/bamtools — Issue #32: potential error in bamtools split function
Author: fyfy
Created: 2012-02-05 03:47:40+00:00
State: open

Dear Derek:
Although I am not 100% sure, I highly suspect that there is a bug in the split BAM function, that a read can be duplicated multiple times (> 20000) in the output BAM files when the input BAM is split by reference chromosomes (HG19). The duplication of read seems randomly occur with 1 to 5% of chances when many jobs were submitted simultaneously to a compute cluster running SGE. What I did or what might cause the problem are:
1) I use it as an application, not a library.
2) multiple "bamtools split" jobs may run on the same node. Only one or a few might have the problem, and if I re-run those files, the results will be OK.
3) "bamtools split" is used in the middle of multiple steps connected through named pipes.

Could you please check the codes to see any possibility of a bug resulting in duplicated reads in rare situations?

Many thanks.

Fan Yang