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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?