How to set the GATK_PATH of PolySolver

Question

[shiyang93]

Hi I want to use PolySolver developed by broadinstitute for HLA typing, when I installed the software, I had to specify the path of GATK directory: GATK_DIR: directory containing the GATK jar files However, after I have set this path and run the example, an error occurred: Error: Unable to access jar file path/to/gatk/SamToFastq.jar

But the GATK only contains a GenomeAnalysisTK.jar, I wonder if there is an older version of GATK which includes many jar files (Possibly now they are packaged into one jar file). Anyone who has used Polysolver could tell me how to run this software corrrectly? Or know which version of GATK should I use? Is there other HLA typing software could be used now?

THANKS A LOT!

[h.mon]

Partially answered on this post from GATK forum.

[shiyang93]

Thanks! I have seen this post before and try, but did not find the correct version. Because I could not find other similar questions/answers on the internet, so I wonder if there is a workaround for running polysolver. Otherwise I think there must be more people who cannot run this software and more questions. Have you run Polysolver successfully? Could you give me some advice?

[h.mon]

I have seen this post before and try

If you did, why did you write your question as if you didn't?

Could you give me some advice?

Use some other software, with a proper source repository other than just a compressed supplementary file, and most important, with clear and detailed installation instructions.

Or contact the authors for support.

Answer 1

[maduh17]

It seems that the software is ridden with many issues. I'm also right now struggling with installation + fixing broken links + fixing file extensions that are missing in the scripts etc. The email provided at the website bounced my email back.