Question: Should I use the same reference indexing command of bwa for WGS and WES analysis?
0
gravatar for maria2019
6 months ago by
maria201930
maria201930 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 • 190 views
ADD COMMENTlink modified 6 months ago by finswimmer12k • written 6 months ago by maria201930
0
gravatar for finswimmer
6 months ago by
finswimmer12k
Germany
finswimmer12k 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 6 months ago by finswimmer12k
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