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I tried executing ParseMako.py file with Python 2.7 and also Python 3.7.3 but nothing happens after executing no matter how I adjust the parameters. I get no output files.

I tried running it on the demo files provided (assuming hg38 reference) and nothing happens.

How does one run the ParseMako file? Thanks.

Hello,

I’m hoping to include Mako in a benchmark of complex SV callers and I wanted to ask about the proper way to interpret Mako’s output in the cases of a few kinds of simple and complex SVs that were mentioned in the paper as being types that are supported by the tool. I’ve run Mako on a simulated genome and have included examples of common forms of output for dispersed duplication, inverted dispersed duplication, translocation, as well as tandem duplication and simple inversion.

• Dispersed duplication

  • substantial majority of / nearly all records came with ‘DEL,DUP’ type label
  • most common cases: nested DEL/DUP or DEL/DEL fragments (both belonging to 'DEL,DUP' typed output records)
    
    

• Translocation

  • substantial majority of / nearly all records came with ‘DEL,DUP’ type label
  • many calls were of the same form as the dominant dispersed dup outputs given above ^, with the most common output form being three DEL frags in the following arrangement
    
    

• Inverted dispersed duplication

  • nearly all records given with type label ‘INV,DEL’
  • most common arrangement of fragments: three fragments of either two INVs and one DEL or two DELs and one INV, with one INV and one DEL covering the same interval
    
    

• Tandem duplication

  • nearly all records given with type label ‘DEL,DUP’, with only a single DEL frag reported
    
    

• Simple inversion

  • nearly all records given with type label ‘INV,DEL’, and reported with two INV fragments and a DEL fragment all covering roughly the same interval
    
    

Since these outputs are fairly persistent in these various cases of each groundtruth SV I’m curious if they’re meant to correspond to those SV types, and if there might be a known mapping between arrangements of typed fragments and complex or simple whole-SV type labels.

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