Interpretation of the output

[ebattistella]

Dear authors,

Thank you very much for this great tool!
I had some questions about interpreting the output vcf file generated by Mako.
First, I wondered how to obtain the types of CSV you report in your article, like Dispersed or tandem events.
Then, I noticed that when trying Mako on NA19240, I obtained variants of CXS=0. How is it possible, according to the definition of complexity you give in your article?
Also, I would want to know the interval for each subcomponent. However, sometimes, a DEL, DUP is reported, but there are several different intervals for DEL and none for the DUP.
For instance, in chr1 at 14,109,719, you can see such a case. Also, the SVLEN is smaller than the interval between the start and end positions.

Could you please give me some details about Mako's output?

Regards,
Enzo Battistella
NA19240_mako.txt

[jiadong324]

Sorry for the late reply.

I found you are using Mako V1.0, please try V1.2.

[ebattistella]

Thank you for your answer.
I am already using version 1.2.
However, I noticed that the file ParseMako.py had not been updated and still reported version 1 on line 119.

[ebattistella]

Dear Jiaodong,

We are very interested in using your tool.
Could you please provide some insight on how to interpret your dispersed and tandem events?
Also, how can we interpret the subinterval?

The file I shared before is already using version 1.2.

Thank you for your help.