Question: Edit distance of an alignment
gravatar for ec_yeh
7 months ago by
ec_yeh0 wrote:

I am new to VG.

I have mapped short sequences to a genome graph using vg map. Now I wish to extract sequences from the result GAM file that are mapped to the genome graph with edit distance less or equal to 2.

Is there a (an easy) way to do it?

If I want to extract the perfect matches instead of the ones with edit distance <= 2 , is (.identity==1) the right condition to use?

variation graph vg • 193 views
ADD COMMENTlink modified 7 months ago by glenn.hickey150 • written 7 months ago by ec_yeh0
gravatar for glenn.hickey
7 months ago by
glenn.hickey150 wrote:

You are probably best to use the "score" field, as "identity" doesn't take into account gaps. The default scoring parameters are displayed under the "scoring:" section if you run vg map without any arguments. With the defaults, a perfect score is 10 + length of the read.

ADD COMMENTlink written 7 months ago by glenn.hickey150
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