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BWA Results Vary Based on Thread Number #1

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DarioS opened this issue Feb 17, 2021 · 2 comments
Open

BWA Results Vary Based on Thread Number #1

DarioS opened this issue Feb 17, 2021 · 2 comments

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@DarioS
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DarioS commented Feb 17, 2021

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
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FYI: root cause issue is lh3/bwa#121

@calizilla
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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.

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@DarioS @d-cameron @calizilla