Question: BWA-MEM rather than bowtie2 in UKBB exome-sequencing alignment
gravatar for Shicheng Guo
5 weeks ago by
Shicheng Guo8.0k
Shicheng Guo8.0k wrote:

Hi All,

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


exome-sequencing • 107 views
ADD COMMENTlink written 5 weeks ago by Shicheng Guo8.0k

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.

ADD REPLYlink written 5 weeks ago by igor9.2k
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