Question: Edit distance of an alignment
0
gravatar for ec_yeh
7 months ago by
ec_yeh0
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
1
gravatar for glenn.hickey
7 months ago by
glenn.hickey150
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1034 users visited in the last hour