Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?