Question: BWA-MEM rather than bowtie2 in UKBB exome-sequencing alignment
gravatar for Shicheng Guo
9 months ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

Hi All,

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


exome-sequencing • 212 views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 9 months ago by Shicheng Guo8.3k

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 9 months ago by igor11k
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