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BWA parameters in gatk4-data-processing workflow

Dear GATK developers,

I'm using the provided WDL script for data preprocessing (https://github.com/gatk-workflows/gatk4-data-processing).
I noticed the BWA parameters are: bwa_commandline="bwa mem -K 100000000 -p -v 3 -t 16 $bash_ref_fasta"

What is the -K flag for? I could not find it in the BWA manual.
Further I'm wondering if the -M flag isn't required anymore?

Thanks
Tim

Tagged:

Issue · Github
by Sheila

Issue Number
2986
State
closed
Last Updated
Assignee
Array
Closed By
sooheelee

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @TimJeske
    Hi Tim,

    I need to check with the team and get back to you.

    -Sheila

  • TimJeskeTimJeske Member

    Thanks for your detailed answer. That helps a lot.

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