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,