BWA Results Vary Based on Thread Number

Sydney-Informatics-Hub / Fastq-to-BAM

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

GNU General Public License v3.0

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BWA Results Vary Based on Thread Number #1

Open DarioS opened 3 years ago

DarioS commented 3 years ago

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 commented 3 years ago

FYI: root cause issue is https://github.com/lh3/bwa/issues/121

calizilla commented 2 years ago

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.