Question

Pindel: RPL structural variation type

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9.6 years ago

iraun 6.2k

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 structural 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 • 4.7k views

ADD COMMENT • link updated 2.3 years ago by Ram 43k • written 9.6 years ago by iraun 6.2k

Ram · Answer 1 · 2014-10-03

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9.6 years ago

Fedor Gusev ▴ 210

Replacement. See this post on seqanswers.

ADD COMMENT • link updated 2.3 years ago by Ram 43k • written 9.6 years ago by Fedor Gusev ▴ 210

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

ADD REPLY • link updated 2.3 years ago by Ram 43k • written 9.6 years ago by iraun 6.2k