Question: Pindel: RPL structural variation type
0
gravatar for iraun
5.7 years ago by
iraun3.7k
Norway
iraun3.7k wrote:

Hi there,
Can anyone explain me what is the meaning of a RPL variation? I have created a deletion of 3000bp manually, and then run pindel to check if pindel can detect it. In the output file I have this line:

 END=8044;HOMLEN=0;SVLEN=-3047;SVTYPE=RPL;NTLEN=47    GT:AD    1/1:15,241

As can be seen, there isn't a deletion, it is a RPL and also, the length of the stuctural variation is 3047 (SVLEN), and NTLEN=47? 3047-47=3000 (the length of my deletion). Anyone can explain me something about this?

Thanks in advance,
 

pindel • 3.0k views
ADD COMMENTlink modified 5.7 years ago by Fedor Gusev210 • written 5.7 years ago by iraun3.7k
2
gravatar for Fedor Gusev
5.7 years ago by
Fedor Gusev210
Russian Federation
Fedor Gusev210 wrote:

Replacement. See this post on seqanswers.

ADD COMMENTlink written 5.7 years ago by Fedor Gusev210

Yes, you are right, thanks. Do you know how can I now the deleted sequence and the inserted one?

ADD REPLYlink written 5.7 years ago by iraun3.7k
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