BWA-MEM rather than bowtie2 in UKBB exome-sequencing alignment

Question

[Shicheng Guo]

Hi All,

Who knows why UKBB applied BWA-MEM rather than bowtie2 for the first 50,000 UKBB exome-sequencing alignment?

Thanks.

[igor]

Were they considering Bowtie2?

I don't know how UKBB chose their pipeline, but most exome sequencing projects (for example, TCGA or gnomAD) use BWA, so it's not a surprising choice.