bwa-mem2 support for reference-flow #5
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Hello,
I added the functionality to use bwa-mem2 aligner instead of bowtie2 in reference-flow pipeline. The default aligner remains to be bowtie2. I haven't uploaded the bwa-mem2 prebuilt index anywhere (it's large) but if the developers can host them like bowtie2 indices, I'd be happy to upload them to the project's AWS data repo.
Other changes:
src/download_1kg_vcf.shnow downloadtbifiles andchrX