Question: Should I use the same reference indexing command of bwa for WGS and WES analysis?
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gravatar for maria2019
10 months ago by
maria201980
maria201980 wrote:

I want to do WGS and WES alignment with BWA mem. Should I use the same reference indexing command for both WES and WGS?

I know that reference indexing for WGS would be: "bwa index -a bwtsw ref.fa"

  • Should I use the command for the WES or I should remove the - a bwtsw and go with "bwa index ref.fa"?
  • Where should I use - a bwtsw option exactly? I know that it is a must for WGS.
wgs bwa mem wes indexing • 272 views
ADD COMMENTlink modified 10 months ago by finswimmer13k • written 10 months ago by maria201980
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gravatar for finswimmer
10 months ago by
finswimmer13k
Germany
finswimmer13k wrote:

Hello,

-a bwtsw describes the algorithm used for constructing the Burrow-Wheeler-Tree of the reference genome. bwa uses different ones for "short" and "long" genomes (Where ever the border is ...). So this is independent of the analysis you are planning.

If you just omit the -a parameter bwa will should the best algorithm automatically.

fin swimmer

ADD COMMENTlink written 10 months ago by finswimmer13k
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