Replace bwa with bwa-mem2

Gleeson-Lab / wxs_pipeline

Starting with BAMs and FASTQs, follow GATK 4.0 Best Practices up to generating a joint-genotyped VCF

1 stars 1 forks source link

Replace bwa with bwa-mem2 #18

Open brcopeland opened 2 years ago

brcopeland commented 2 years ago

Per https://github.com/bwa-mem2/bwa-mem2, bwa-mem2 is a drop-in replacement that is ~1.3-3.1x faster than bwa mem. This can be done by simply replacing bwa/mem in the wrapper section of the rule with bwa-mem2/mem.