BWA Results Vary Based on Thread Number

[DarioS]

Threads Used Affects Results

OK, the root cause is that bwa 0.7.17-r1188 MAPQ scores are not stable w.r.t to number of threads used to run bwa.

[ds6924@gadi-login-06 ~]$ module load bwa
[ds6924@gadi-login-06 ~]$ bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li <lh3@sanger.ac.uk>

Should -K be set in align.sh?

[d-cameron]

FYI: root cause issue is lh3/bwa#121

[calizilla]

Feel free to set a high K as per Heng Li's advice on the above issue eg -K 10000000. I won't update the align.sh script with that until I have time to test for any performance changes.