extract coordinates

[adriludwig]

Hi! I'm wondering if there is a tool to extract the coordinates of the possible insertions. Thanks!

[Mesh89]

Hi. I am not sure I understand your question. The coordinates are explicitly reported, for example

ID=1 BP1=F:chr5:135114483 BP2=R:chr12:59936709 DISCORDANT=66 SCORE=2.275862
ID=1 BP1=R:chr5:135114528 BP2=F:chr12:59937336 DISCORDANT=55 SCORE=3.666667

Region chr12:59936709-59937336 is inserted into chr5:135114483-135114528

You can see the README for an explanation of the output.

BTW, we have a much improved newly released tool: https://github.com/kensung-lab/INSurVeyor
It reports insertions (including the inserted sequence) directly in VCF format, which may be much easier to interpret.